Merge branch 'graphs4value:main' into datastructure

634 files changed, 20558 insertions, 3932 deletions

diff --git a/subprojects/frontend/.eslintrc.cjs b/subprojects/frontend/.eslintrc.cjs
index 8a7b474a..25b86a83 100644
--- a/subprojects/frontend/.eslintrc.cjs
+++ b/subprojects/frontend/.eslintrc.cjs
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 const path = require('node:path');
 
 // Allow the Codium ESLint plugin to find `tsconfig.json` from the repository root.
@@ -43,6 +49,15 @@ module.exports = {
     // In typescript, some class methods implementing an inderface do not use `this`:
     // https://github.com/typescript-eslint/typescript-eslint/issues/1103
     'class-methods-use-this': 'off',
+    // Disable rules with a high performance cost.
+    // See https://typescript-eslint.io/linting/troubleshooting/performance-troubleshooting/
+    'import/default': 'off',
+    'import/extensions': 'off',
+    'import/named': 'off',
+    'import/namespace': 'off',
+    'import/no-named-as-default': 'off',
+    'import/no-named-as-default-member': 'off',
+    '@typescript-eslint/indent': 'off',
     // Make sure every import can be resolved by `eslint-import-resolver-typescript`.
     'import/no-unresolved': 'error',
     // Organize imports automatically.
@@ -90,6 +105,7 @@ module.exports = {
       files: [
         '.eslintrc.cjs',
         'config/*.ts',
+        'config/*.cjs',
         'prettier.config.cjs',
         'vite.config.ts',
       ],
@@ -103,6 +119,8 @@ module.exports = {
           'error',
           { devDependencies: true },
         ],
+        // Allow writing to the console in ad-hoc scripts.
+        'no-console': 'off',
         // Access to the environment in configuration files.
         'no-process-env': 'off',
       },
diff --git a/subprojects/frontend/assets-src/favicon.svg.license b/subprojects/frontend/assets-src/favicon.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/assets-src/favicon.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/assets-src/icon.svg.license b/subprojects/frontend/assets-src/icon.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/assets-src/icon.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/assets-src/mask-icon.svg.license b/subprojects/frontend/assets-src/mask-icon.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/assets-src/mask-icon.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/build.gradle b/subprojects/frontend/build.gradle
deleted file mode 100644
index 4cc2c5d7..00000000
--- a/subprojects/frontend/build.gradle
+++ /dev/null
@@ -1,131 +0,0 @@
-plugins {
-        id 'refinery-frontend-workspace'
-        id 'refinery-sonarqube'
-}
-
-import org.siouan.frontendgradleplugin.infrastructure.gradle.RunYarn
-
-def viteOutputDir = "${buildDir}/vite"
-def productionResources = file("${viteOutputDir}/production")
-
-frontend {
-        assembleScript = 'run build'
-}
-
-configurations {
-        productionAssets {
-                canBeConsumed = true
-                canBeResolved = false
-        }
-}
-
-def installFrontend = tasks.named('installFrontend')
-
-def sourcesWithoutTypegen = fileTree('src') {
-        exclude '**/*.typegen.ts'
-}
-
-def assembleFrontend = tasks.named('assembleFrontend')
-assembleFrontend.configure {
-        dependsOn generateXStateTypes
-        inputs.dir 'public'
-        inputs.files sourcesWithoutTypegen
-        inputs.file 'index.html'
-        inputs.files('package.json', 'tsconfig.json', 'tsconfig.base.json', 'vite.config.ts')
-        inputs.file rootProject.file('yarn.lock')
-        outputs.dir productionResources
-}
-
-artifacts {
-        productionAssets(productionResources) {
-                builtBy assembleFrontend
-        }
-}
-
-def generateXStateTypes = tasks.register('generateXStateTypes', RunYarn) {
-        dependsOn installFrontend
-        inputs.files sourcesWithoutTypegen
-        inputs.file 'package.json'
-        inputs.file rootProject.file('yarn.lock')
-        outputs.dir 'src'
-        script = 'run typegen'
-        description = 'Generate TypeScript typings for XState state machines.'
-}
-
-def typecheckFrontend = tasks.register('typecheckFrontend', RunYarn) {
-        dependsOn installFrontend
-        dependsOn generateXStateTypes
-        inputs.dir 'src'
-        inputs.dir 'types'
-        inputs.files('package.json', 'tsconfig.json', 'tsconfig.base.json', 'tsconfig.node.json')
-        inputs.file rootProject.file('yarn.lock')
-        outputs.dir "${buildDir}/typescript"
-        script = 'run typecheck'
-        group = 'verification'
-        description = 'Check for TypeScript type errors.'
-}
-
-def lintFrontend = tasks.register('lintFrontend', RunYarn) {
-        dependsOn installFrontend
-        dependsOn generateXStateTypes
-        dependsOn typecheckFrontend
-        inputs.dir 'src'
-        inputs.dir 'types'
-        inputs.files('.eslintrc.cjs', 'prettier.config.cjs')
-        inputs.files('package.json', 'tsconfig.json', 'tsconfig.base.json', 'tsconfig.node.json')
-        inputs.file rootProject.file('yarn.lock')
-        if (project.hasProperty('ci')) {
-                outputs.file "${buildDir}/eslint.json"
-                script = 'run lint:ci'
-        } else {
-                script = 'run lint'
-        }
-        group = 'verification'
-        description = 'Check for TypeScript lint errors and warnings.'
-}
-
-def prettier = tasks.register('fixFrontend', RunYarn) {
-        dependsOn installFrontend
-        dependsOn generateXStateTypes
-        dependsOn typecheckFrontend
-        inputs.dir 'src'
-        inputs.dir 'types'
-        inputs.files('.eslintrc.cjs', 'prettier.config.cjs')
-        inputs.files('package.json', 'tsconfig.json', 'tsconfig.base.json', 'tsconfig.node.json')
-        inputs.file rootProject.file('yarn.lock')
-        script = 'run lint:fix'
-        group = 'verification'
-        description = 'Fix TypeScript lint errors and warnings.'
-}
-
-tasks.named('check') {
-        dependsOn(typecheckFrontend)
-        dependsOn(lintFrontend)
-}
-
-tasks.register('serveFrontend', RunYarn) {
-        dependsOn installFrontend
-        dependsOn generateXStateTypes
-        inputs.dir 'public'
-        inputs.files sourcesWithoutTypegen
-        inputs.file 'index.html'
-        inputs.files('package.json', 'tsconfig.json', 'tsconfig.base.json', 'vite.config.ts')
-        inputs.file rootProject.file('yarn.lock')
-        outputs.dir "${viteOutputDir}/development"
-        script = 'run serve'
-        group = 'run'
-        description = 'Start a Vite dev server with hot module replacement.'
-}
-
-tasks.named('clean') {
-        delete 'dev-dist'
-        delete fileTree('src') {
-                include '**/*.typegen.ts'
-        }
-}
-
-sonarqube.properties {
-        properties['sonar.sources'] = 'src'
-        property 'sonar.nodejs.executable', "${frontend.nodeInstallDirectory.get()}/bin/node"
-        property 'sonar.eslint.reportPaths', "${buildDir}/eslint.json"
-}
diff --git a/subprojects/frontend/build.gradle.kts b/subprojects/frontend/build.gradle.kts
new file mode 100644
index 00000000..d0839371
--- /dev/null
+++ b/subprojects/frontend/build.gradle.kts
@@ -0,0 +1,144 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+import org.siouan.frontendgradleplugin.infrastructure.gradle.RunYarn
+import tools.refinery.gradle.utils.SonarPropertiesUtils
+
+plugins {
+        id("tools.refinery.gradle.frontend-workspace")
+        id("tools.refinery.gradle.sonarqube")
+}
+
+frontend {
+        assembleScript.set("run build")
+}
+
+val viteOutputDir = "$buildDir/vite"
+
+val productionResources = file("$viteOutputDir/production")
+
+val productionAssets: Configuration by configurations.creating {
+        isCanBeConsumed = true
+        isCanBeResolved = false
+}
+
+val sourcesWithoutTypes = fileTree("src") {
+        exclude("**/*.typegen.ts")
+}
+
+val sourcesWithTypes: FileCollection = fileTree("src") + fileTree("types")
+
+val buildScripts: FileCollection = fileTree("config") + files(
+                ".eslintrc.cjs",
+                "prettier.config.cjs",
+                "vite.config.ts",
+)
+
+val installationState = files(
+                rootProject.file("yarn.lock"),
+                rootProject.file("package.json"),
+                "package.json",
+)
+
+val sharedConfigFiles: FileCollection = installationState + files(
+                "tsconfig.json",
+                "tsconfig.base.json",
+                "tsconfig.node.json",
+                "tsconfig.shared.json",
+)
+
+val assembleConfigFiles = sharedConfigFiles + file("vite.config.ts") + fileTree("config") {
+        include("**/*.ts")
+}
+
+val assembleSources = sourcesWithTypes + fileTree("public") + file("index.html")
+
+val assembleFiles = assembleSources + assembleConfigFiles
+
+val lintingFiles: FileCollection = sourcesWithTypes + buildScripts + sharedConfigFiles
+
+tasks {
+        val generateXStateTypes by registering(RunYarn::class) {
+                dependsOn(installFrontend)
+                inputs.files(sourcesWithoutTypes)
+                inputs.files(installationState)
+                outputs.dir("src")
+                script.set("run typegen")
+                description = "Generate TypeScript typings for XState state machines."
+        }
+
+        assembleFrontend {
+                dependsOn(generateXStateTypes)
+                inputs.files(assembleFiles)
+                outputs.dir(productionResources)
+        }
+
+
+        val typeCheckFrontend by registering(RunYarn::class) {
+                dependsOn(installFrontend)
+                dependsOn(generateXStateTypes)
+                inputs.files(lintingFiles)
+                outputs.dir("$buildDir/typescript")
+                script.set("run typecheck")
+                group = "verification"
+                description = "Check for TypeScript type errors."
+        }
+
+        val lintFrontend by registering(RunYarn::class) {
+                dependsOn(installFrontend)
+                dependsOn(generateXStateTypes)
+                dependsOn(typeCheckFrontend)
+                inputs.files(lintingFiles)
+                outputs.file("$buildDir/eslint.json")
+                script.set("run lint")
+                group = "verification"
+                description = "Check for TypeScript lint errors and warnings."
+        }
+
+        register<RunYarn>("fixFrontend") {
+                dependsOn(installFrontend)
+                dependsOn(generateXStateTypes)
+                dependsOn(typeCheckFrontend)
+                inputs.files(lintingFiles)
+                script.set("run lint:fix")
+                group = "verification"
+                description = "Fix TypeScript lint errors and warnings."
+        }
+
+        check {
+                dependsOn(typeCheckFrontend)
+                dependsOn(lintFrontend)
+        }
+
+        register<RunYarn>("serveFrontend") {
+                dependsOn(installFrontend)
+                dependsOn(generateXStateTypes)
+                inputs.files(assembleFiles)
+                outputs.dir("$viteOutputDir/development")
+                script.set("run serve")
+                group = "run"
+                description = "Start a Vite dev server with hot module replacement."
+        }
+
+        clean {
+                delete("dev-dist")
+                delete(fileTree("src") {
+                        include("**/*.typegen.ts")
+                })
+        }
+}
+
+artifacts {
+        add("productionAssets", productionResources) {
+                builtBy(tasks.assembleFrontend)
+        }
+}
+
+sonarqube.properties {
+        SonarPropertiesUtils.addToList(properties, "sonar.sources", "src")
+        property("sonar.nodejs.executable", "${frontend.nodeInstallDirectory.get()}/bin/node")
+        property("sonar.eslint.reportPaths", "$buildDir/eslint.json")
+}
diff --git a/subprojects/frontend/config/backendConfigVitePlugin.ts b/subprojects/frontend/config/backendConfigVitePlugin.ts
index 7a6bc3db..3bffce3a 100644
--- a/subprojects/frontend/config/backendConfigVitePlugin.ts
+++ b/subprojects/frontend/config/backendConfigVitePlugin.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { PluginOption } from 'vite';
 
 import type BackendConfig from '../src/xtext/BackendConfig';
diff --git a/subprojects/frontend/config/detectDevModeOptions.ts b/subprojects/frontend/config/detectDevModeOptions.ts
index b3696241..665204dc 100644
--- a/subprojects/frontend/config/detectDevModeOptions.ts
+++ b/subprojects/frontend/config/detectDevModeOptions.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { PluginOption, ServerOptions } from 'vite';
 
 import backendConfigVitePlugin, {
diff --git a/subprojects/frontend/config/eslintReport.cjs b/subprojects/frontend/config/eslintReport.cjs
new file mode 100644
index 00000000..7c4b7bd6
--- /dev/null
+++ b/subprojects/frontend/config/eslintReport.cjs
@@ -0,0 +1,58 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+const { writeFile } = require('node:fs/promises');
+const path = require('node:path');
+const { Readable } = require('node:stream');
+const { pipeline } = require('node:stream/promises');
+
+const { ESLint } = require('eslint');
+
+const rootDir = path.join(__dirname, '..');
+
+/**
+ * Write ESLint report to console.
+ *
+ * @param cli {import('eslint').ESLint} The ESLint CLI.
+ * @param report {import('eslint').ESLint.LintResult[]} The ESLint report.
+ * @return {Promise<void>} A promise that resolves when the report is finished.
+ */
+async function reportToConsole(cli, report) {
+  const stylishFormatter = await cli.loadFormatter('stylish');
+  const output = new Readable();
+  output.push(await stylishFormatter.format(report));
+  output.push(null);
+  return pipeline(output, process.stdout);
+}
+
+/**
+ * Write ESLint report to the <code>build</code> directory.
+ *
+ * @param cli {import('eslint').ESLint} The ESLint CLI.
+ * @param report {import('eslint').ESLint.LintResult[]} The ESLint report.
+ * @return {Promise<void>} A promise that resolves when the report is finished.
+ */
+async function reportToJson(cli, report) {
+  const jsonFormatter = await cli.loadFormatter('json');
+  const json = await jsonFormatter.format(report);
+  const reportPath = path.join(rootDir, 'build', 'eslint.json');
+  return writeFile(reportPath, json, 'utf-8');
+}
+
+async function createReport() {
+  const cli = new ESLint({
+    useEslintrc: true,
+    cwd: rootDir,
+  });
+  const report = await cli.lintFiles('.');
+  await Promise.all([reportToConsole(cli, report), reportToJson(cli, report)]);
+
+  if (report.some((entry) => entry.errorCount > 0)) {
+    process.exitCode = 1;
+  }
+}
+
+createReport().catch(console.error);
diff --git a/subprojects/frontend/config/fetchPackageMetadata.ts b/subprojects/frontend/config/fetchPackageMetadata.ts
index 50807b03..02e16d57 100644
--- a/subprojects/frontend/config/fetchPackageMetadata.ts
+++ b/subprojects/frontend/config/fetchPackageMetadata.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { readFile } from 'node:fs/promises';
 import path from 'node:path';
 
diff --git a/subprojects/frontend/config/manifest.ts b/subprojects/frontend/config/manifest.ts
index 3cec777c..1822dc7c 100644
--- a/subprojects/frontend/config/manifest.ts
+++ b/subprojects/frontend/config/manifest.ts
@@ -1,10 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { ManifestOptions } from 'vite-plugin-pwa';
 
 const manifest: Partial<ManifestOptions> = {
   lang: 'en-US',
   name: 'Refinery',
   short_name: 'Refinery',
-  description: 'An efficient graph sovler for generating well-formed models',
+  description: 'An efficient graph solver for generating well-formed models',
   theme_color: '#f5f5f5',
   display_override: ['window-controls-overlay'],
   display: 'standalone',
diff --git a/subprojects/frontend/config/minifyHTMLVitePlugin.ts b/subprojects/frontend/config/minifyHTMLVitePlugin.ts
index 18336d4d..7c08c488 100644
--- a/subprojects/frontend/config/minifyHTMLVitePlugin.ts
+++ b/subprojects/frontend/config/minifyHTMLVitePlugin.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { minify, type Options as TerserOptions } from 'html-minifier-terser';
 import type { PluginOption } from 'vite';
 
diff --git a/subprojects/frontend/config/preloadFontsVitePlugin.ts b/subprojects/frontend/config/preloadFontsVitePlugin.ts
index bc6f8eaf..5c04477a 100644
--- a/subprojects/frontend/config/preloadFontsVitePlugin.ts
+++ b/subprojects/frontend/config/preloadFontsVitePlugin.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import micromatch from 'micromatch';
 import type { PluginOption } from 'vite';
 
diff --git a/subprojects/frontend/index.html b/subprojects/frontend/index.html
index 8b6814eb..1bf3472e 100644
--- a/subprojects/frontend/index.html
+++ b/subprojects/frontend/index.html
@@ -1,4 +1,9 @@
 <!DOCTYPE html>
+<!--
+  SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+  SPDX-License-Identifier: EPL-2.0
+-->
 <html lang="en-US">
   <head>
     <meta charset="utf-8">
@@ -13,9 +18,9 @@
     <meta name="theme-color" media="(prefers-color-scheme:light)" content="#f5f5f5">
     <meta name="theme-color" media="(prefers-color-scheme:dark)" content="#21252b">
     <style>
-      @import '@fontsource/inter/variable.css';
-      @import '@fontsource/jetbrains-mono/variable.css';
-      @import '@fontsource/jetbrains-mono/variable-italic.css';
+      @import '@fontsource-variable/inter/wght.css';
+      @import '@fontsource-variable/jetbrains-mono/wght.css';
+      @import '@fontsource-variable/jetbrains-mono/wght-italic.css';
     </style>
   </head>
   <body>
diff --git a/subprojects/frontend/package.json b/subprojects/frontend/package.json
index a9153cd4..ba8a0a58 100644
--- a/subprojects/frontend/package.json
+++ b/subprojects/frontend/package.json
@@ -1,94 +1,99 @@
 {
+  "//": [
+    "SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>",
+    "",
+    "SPDX-License-Identifier: EPL-2.0"
+  ],
   "name": "@refinery/frontend",
   "version": "0.0.0",
   "description": "Web frontend for Refinery",
+  "type": "module",
   "private": true,
   "scripts": {
     "build": "cross-env MODE=production vite build",
     "serve": "cross-env MODE=development vite serve",
     "typegen": "xstate typegen \"src/**/*.ts?(x)\"",
     "typecheck": "tsc -p tsconfig.shared.json && tsc -p tsconfig.node.json && tsc -p tsconfig.json",
-    "lint": "eslint .",
-    "lint:ci": "eslint -f json -o build/eslint.json .",
+    "lint": "node config/eslintReport.cjs",
     "lint:fix": "yarn run lint --fix"
   },
   "repository": {
     "type": "git",
     "url": "git+https://github.com/graphs4value/refinery.git"
   },
-  "author": "Refinery authors",
+  "author": "The Refinery Authors <https://refinery.tools/>",
   "license": "EPL-2.0",
   "bugs": {
-    "url": "https://github.com/graphs4value/issues"
+    "url": "https://github.com/graphs4value/refinery/issues"
   },
   "homepage": "https://refinery.tools",
   "dependencies": {
-    "@codemirror/autocomplete": "^6.4.0",
-    "@codemirror/commands": "^6.2.0",
-    "@codemirror/language": "^6.4.0",
-    "@codemirror/lint": "^6.1.0",
-    "@codemirror/search": "^6.2.3",
-    "@codemirror/state": "^6.2.0",
-    "@codemirror/view": "^6.7.3",
-    "@emotion/react": "^11.10.5",
-    "@emotion/styled": "^11.10.5",
-    "@fontsource/inter": "^4.5.15",
-    "@fontsource/jetbrains-mono": "^4.5.12",
-    "@lezer/common": "^1.0.2",
-    "@lezer/highlight": "^1.1.3",
-    "@lezer/lr": "^1.3.3",
+    "@codemirror/autocomplete": "^6.8.0",
+    "@codemirror/commands": "^6.2.4",
+    "@codemirror/language": "^6.8.0",
+    "@codemirror/lint": "^6.2.2",
+    "@codemirror/search": "^6.5.0",
+    "@codemirror/state": "^6.2.1",
+    "@codemirror/view": "^6.13.2",
+    "@emotion/react": "^11.11.1",
+    "@emotion/styled": "^11.11.0",
+    "@fontsource-variable/inter": "^5.0.3",
+    "@fontsource-variable/jetbrains-mono": "^5.0.3",
+    "@lezer/common": "^1.0.3",
+    "@lezer/highlight": "^1.1.6",
+    "@lezer/lr": "^1.3.6",
     "@material-icons/svg": "^1.0.33",
-    "@mui/icons-material": "5.11.0",
-    "@mui/material": "5.11.7",
-    "@vitejs/plugin-react-swc": "^3.1.0",
+    "@mui/icons-material": "5.11.16",
+    "@mui/material": "5.13.5",
+    "@vitejs/plugin-react-swc": "^3.3.2",
     "ansi-styles": "^6.2.1",
+    "csstype": "^3.1.2",
     "escape-string-regexp": "^5.0.0",
     "lodash-es": "^4.17.21",
     "loglevel": "^1.8.1",
     "loglevel-plugin-prefix": "^0.8.4",
-    "mobx": "^6.7.0",
-    "mobx-react-lite": "^3.4.0",
+    "mobx": "^6.9.0",
+    "mobx-react-lite": "^3.4.3",
     "ms": "^2.1.3",
-    "nanoid": "^4.0.0",
-    "notistack": "^2.0.8",
+    "nanoid": "^4.0.2",
+    "notistack": "^3.0.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "xstate": "^4.35.4",
-    "zod": "^3.20.2"
+    "xstate": "^4.37.2",
+    "zod": "^3.21.4"
   },
   "devDependencies": {
-    "@lezer/generator": "^1.2.2",
-    "@tsconfig/node18-strictest-esm": "^1.0.1",
-    "@types/eslint": "^8.21.0",
+    "@lezer/generator": "^1.3.0",
+    "@types/eslint": "^8.40.2",
     "@types/html-minifier-terser": "^7.0.0",
-    "@types/lodash-es": "^4.17.6",
+    "@types/lodash-es": "^4.17.7",
     "@types/micromatch": "^4.0.2",
     "@types/ms": "^0.7.31",
-    "@types/node": "^18.11.18",
-    "@types/prettier": "^2.7.2",
-    "@types/react": "^18.0.27",
-    "@types/react-dom": "^18.0.10",
-    "@typescript-eslint/eslint-plugin": "^5.50.0",
-    "@typescript-eslint/parser": "^5.50.0",
-    "@xstate/cli": "^0.4.2",
+    "@types/node": "^18.16.18",
+    "@types/prettier": "^2.7.3",
+    "@types/react": "^18.2.12",
+    "@types/react-dom": "^18.2.5",
+    "@typescript-eslint/eslint-plugin": "^5.59.11",
+    "@typescript-eslint/parser": "^5.59.11",
+    "@xstate/cli": "^0.5.1",
     "cross-env": "^7.0.3",
-    "eslint": "^8.33.0",
+    "eslint": "^8.43.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-config-airbnb-typescript": "^17.0.0",
-    "eslint-config-prettier": "^8.6.0",
-    "eslint-import-resolver-typescript": "^3.5.3",
+    "eslint-config-prettier": "^8.8.0",
+    "eslint-import-resolver-typescript": "^3.5.5",
     "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-jsx-a11y": "^6.7.1",
     "eslint-plugin-mobx": "^0.0.9",
     "eslint-plugin-prettier": "^4.2.1",
     "eslint-plugin-react": "^7.32.2",
     "eslint-plugin-react-hooks": "^4.6.0",
-    "html-minifier-terser": "^7.1.0",
+    "html-minifier-terser": "^7.2.0",
     "micromatch": "^4.0.5",
-    "prettier": "^2.8.3",
-    "typescript": "4.9.5",
-    "vite": "^4.1.1",
-    "vite-plugin-pwa": "^0.14.1",
-    "workbox-window": "^6.5.4"
+    "prettier": "^2.8.8",
+    "typescript": "5.1.3",
+    "vite": "^4.3.9",
+    "vite-plugin-pwa": "^0.16.4",
+    "workbox-window": "^7.0.0"
   }
 }
diff --git a/subprojects/frontend/prettier.config.cjs b/subprojects/frontend/prettier.config.cjs
index 75f5c54d..6f9ff7ad 100644
--- a/subprojects/frontend/prettier.config.cjs
+++ b/subprojects/frontend/prettier.config.cjs
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 /** @type {import('prettier').Config} */
 module.exports = {
   singleQuote: true,
diff --git a/subprojects/frontend/public/apple-touch-icon.png.license b/subprojects/frontend/public/apple-touch-icon.png.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/apple-touch-icon.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/favicon-96x96.png.license b/subprojects/frontend/public/favicon-96x96.png.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/favicon-96x96.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/favicon.png.license b/subprojects/frontend/public/favicon.png.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/favicon.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/favicon.svg.license b/subprojects/frontend/public/favicon.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/favicon.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/icon-192x192.png.license b/subprojects/frontend/public/icon-192x192.png.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/icon-192x192.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/icon-512x512.png.license b/subprojects/frontend/public/icon-512x512.png.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/icon-512x512.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/icon-any.svg.license b/subprojects/frontend/public/icon-any.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/icon-any.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/mask-icon.svg.license b/subprojects/frontend/public/mask-icon.svg.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/frontend/public/mask-icon.svg.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/frontend/public/robots.txt b/subprojects/frontend/public/robots.txt
index c2a49f4f..e7c73099 100644
--- a/subprojects/frontend/public/robots.txt
+++ b/subprojects/frontend/public/robots.txt
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+#
+# SPDX-License-Identifier: CC0-1.0
+
 User-agent: *
 Allow: /
diff --git a/subprojects/frontend/src/App.tsx b/subprojects/frontend/src/App.tsx
index cd394345..7f242529 100644
--- a/subprojects/frontend/src/App.tsx
+++ b/subprojects/frontend/src/App.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Box from '@mui/material/Box';
 import CssBaseline from '@mui/material/CssBaseline';
 import { throttle } from 'lodash-es';
diff --git a/subprojects/frontend/src/Loading.tsx b/subprojects/frontend/src/Loading.tsx
index 489563e0..adee4f0e 100644
--- a/subprojects/frontend/src/Loading.tsx
+++ b/subprojects/frontend/src/Loading.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import CircularProgress from '@mui/material/CircularProgress';
 import { styled } from '@mui/material/styles';
 
diff --git a/subprojects/frontend/src/PWAStore.ts b/subprojects/frontend/src/PWAStore.ts
index e9f99e2a..a1b3ffd9 100644
--- a/subprojects/frontend/src/PWAStore.ts
+++ b/subprojects/frontend/src/PWAStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { makeAutoObservable, observable } from 'mobx';
 import ms from 'ms';
 // eslint-disable-next-line import/no-unresolved -- Importing virtual module.
diff --git a/subprojects/frontend/src/Refinery.tsx b/subprojects/frontend/src/Refinery.tsx
index 93a82ee1..b5ff94e1 100644
--- a/subprojects/frontend/src/Refinery.tsx
+++ b/subprojects/frontend/src/Refinery.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Grow from '@mui/material/Grow';
 import Stack from '@mui/material/Stack';
 import { SnackbarProvider } from 'notistack';
@@ -8,7 +14,6 @@ import EditorPane from './editor/EditorPane';
 
 export default function Refinery(): JSX.Element {
   return (
-    // @ts-expect-error -- notistack has problems with `exactOptionalPropertyTypes
     <SnackbarProvider TransitionComponent={Grow}>
       <UpdateNotification />
       <Stack direction="column" height="100%" overflow="auto">
diff --git a/subprojects/frontend/src/RootStore.ts b/subprojects/frontend/src/RootStore.ts
index 2e76d66d..b84c0ce0 100644
--- a/subprojects/frontend/src/RootStore.ts
+++ b/subprojects/frontend/src/RootStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { getLogger } from 'loglevel';
 import { makeAutoObservable, runInAction } from 'mobx';
 
diff --git a/subprojects/frontend/src/RootStoreProvider.tsx b/subprojects/frontend/src/RootStoreProvider.tsx
index 2c11a0f9..7cb89af1 100644
--- a/subprojects/frontend/src/RootStoreProvider.tsx
+++ b/subprojects/frontend/src/RootStoreProvider.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { type ReactNode, createContext, useContext } from 'react';
 
 import type RootStore from './RootStore';
diff --git a/subprojects/frontend/src/ToggleDarkModeButton.tsx b/subprojects/frontend/src/ToggleDarkModeButton.tsx
index 59714f20..7a835e61 100644
--- a/subprojects/frontend/src/ToggleDarkModeButton.tsx
+++ b/subprojects/frontend/src/ToggleDarkModeButton.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import DarkModeIcon from '@mui/icons-material/DarkMode';
 import LightModeIcon from '@mui/icons-material/LightMode';
 import IconButton from '@mui/material/IconButton';
diff --git a/subprojects/frontend/src/TopBar.tsx b/subprojects/frontend/src/TopBar.tsx
index 5a825512..f2542b14 100644
--- a/subprojects/frontend/src/TopBar.tsx
+++ b/subprojects/frontend/src/TopBar.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import GitHubIcon from '@mui/icons-material/GitHub';
 import AppBar from '@mui/material/AppBar';
 import Button from '@mui/material/Button';
diff --git a/subprojects/frontend/src/UpdateNotification.tsx b/subprojects/frontend/src/UpdateNotification.tsx
index 07f7f5f7..d86c0703 100644
--- a/subprojects/frontend/src/UpdateNotification.tsx
+++ b/subprojects/frontend/src/UpdateNotification.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Button from '@mui/material/Button';
 import { observer } from 'mobx-react-lite';
 import { useEffect } from 'react';
@@ -32,14 +38,14 @@ export default observer(function UpdateNotification(): null {
       return enqueueLater('Failed to download update', {
         variant: 'error',
         action: (
-          <>
+          <ContrastThemeProvider>
             <Button color="inherit" onClick={() => pwaStore.checkForUpdates()}>
               Try again
             </Button>
             <Button color="inherit" onClick={() => pwaStore.dismissError()}>
               Dismiss
             </Button>
-          </>
+          </ContrastThemeProvider>
         ),
       });
     }
diff --git a/subprojects/frontend/src/WindowControlsOverlayColor.tsx b/subprojects/frontend/src/WindowControlsOverlayColor.tsx
index 14eda566..cfa468ea 100644
--- a/subprojects/frontend/src/WindowControlsOverlayColor.tsx
+++ b/subprojects/frontend/src/WindowControlsOverlayColor.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { useTheme } from '@mui/material/styles';
 import { useEffect } from 'react';
 
diff --git a/subprojects/frontend/src/editor/AnimatedButton.tsx b/subprojects/frontend/src/editor/AnimatedButton.tsx
index f75d4617..dbbda618 100644
--- a/subprojects/frontend/src/editor/AnimatedButton.tsx
+++ b/subprojects/frontend/src/editor/AnimatedButton.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Box from '@mui/material/Box';
 import Button from '@mui/material/Button';
 import { styled, type SxProps, type Theme } from '@mui/material/styles';
diff --git a/subprojects/frontend/src/editor/ConnectButton.tsx b/subprojects/frontend/src/editor/ConnectButton.tsx
index e2d251f3..eed6fbc7 100644
--- a/subprojects/frontend/src/editor/ConnectButton.tsx
+++ b/subprojects/frontend/src/editor/ConnectButton.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import CloudIcon from '@mui/icons-material/Cloud';
 import CloudOffIcon from '@mui/icons-material/CloudOff';
 import SyncIcon from '@mui/icons-material/Sync';
diff --git a/subprojects/frontend/src/editor/ConnectionStatusNotification.tsx b/subprojects/frontend/src/editor/ConnectionStatusNotification.tsx
index 9b27f45c..b7b962ab 100644
--- a/subprojects/frontend/src/editor/ConnectionStatusNotification.tsx
+++ b/subprojects/frontend/src/editor/ConnectionStatusNotification.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Button from '@mui/material/Button';
 import { observer } from 'mobx-react-lite';
 import { useEffect } from 'react';
diff --git a/subprojects/frontend/src/editor/DiagnosticValue.ts b/subprojects/frontend/src/editor/DiagnosticValue.ts
index b4e0b165..20478262 100644
--- a/subprojects/frontend/src/editor/DiagnosticValue.ts
+++ b/subprojects/frontend/src/editor/DiagnosticValue.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { Diagnostic } from '@codemirror/lint';
 import { RangeValue } from '@codemirror/state';
 
diff --git a/subprojects/frontend/src/editor/EditorArea.tsx b/subprojects/frontend/src/editor/EditorArea.tsx
index cfb988b2..905fa2ec 100644
--- a/subprojects/frontend/src/editor/EditorArea.tsx
+++ b/subprojects/frontend/src/editor/EditorArea.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Box from '@mui/material/Box';
 import { useTheme } from '@mui/material/styles';
 import { observer } from 'mobx-react-lite';
diff --git a/subprojects/frontend/src/editor/EditorButtons.tsx b/subprojects/frontend/src/editor/EditorButtons.tsx
index 53b06e23..9b187e5c 100644
--- a/subprojects/frontend/src/editor/EditorButtons.tsx
+++ b/subprojects/frontend/src/editor/EditorButtons.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { Diagnostic } from '@codemirror/lint';
 import CheckIcon from '@mui/icons-material/Check';
 import ErrorIcon from '@mui/icons-material/Error';
diff --git a/subprojects/frontend/src/editor/EditorPane.tsx b/subprojects/frontend/src/editor/EditorPane.tsx
index f7f8241a..87f408fe 100644
--- a/subprojects/frontend/src/editor/EditorPane.tsx
+++ b/subprojects/frontend/src/editor/EditorPane.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Box from '@mui/material/Box';
 import Skeleton from '@mui/material/Skeleton';
 import Stack from '@mui/material/Stack';
diff --git a/subprojects/frontend/src/editor/EditorStore.ts b/subprojects/frontend/src/editor/EditorStore.ts
index 0a0d885d..b98f085e 100644
--- a/subprojects/frontend/src/editor/EditorStore.ts
+++ b/subprojects/frontend/src/editor/EditorStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type {
   CompletionContext,
   CompletionResult,
diff --git a/subprojects/frontend/src/editor/EditorTheme.ts b/subprojects/frontend/src/editor/EditorTheme.ts
index 01b65a7e..e057ce18 100644
--- a/subprojects/frontend/src/editor/EditorTheme.ts
+++ b/subprojects/frontend/src/editor/EditorTheme.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import errorSVG from '@material-icons/svg/svg/error/baseline.svg?raw';
 import expandMoreSVG from '@material-icons/svg/svg/expand_more/baseline.svg?raw';
 import infoSVG from '@material-icons/svg/svg/info/baseline.svg?raw';
@@ -8,32 +14,6 @@ function svgURL(svg: string): string {
   return `url('data:image/svg+xml;utf8,${svg}')`;
 }
 
-function radialShadowTheme(
-  origin: string,
-  scaleX: boolean,
-  scaleY: boolean,
-): CSSObject {
-  function radialGradient(opacity: number, scale: string): string {
-    return `radial-gradient(
-        farthest-side at ${origin},
-        rgba(0, 0, 0, ${opacity}),
-        rgba(0, 0, 0, 0)
-      )
-      ${origin} /
-      ${scaleX ? scale : '100%'}
-      ${scaleY ? scale : '100%'}
-      no-repeat`;
-  }
-
-  return {
-    background: `
-      ${radialGradient(0.2, '40%')},
-      ${radialGradient(0.14, '50%')},
-      ${radialGradient(0.12, '100%')}
-    `,
-  };
-}
-
 export default styled('div', {
   name: 'EditorTheme',
   shouldForwardProp: (propName) =>
@@ -52,98 +32,13 @@ export default styled('div', {
     },
   };
 
-  const scrollerThumbOpacity = theme.palette.mode === 'dark' ? 0.16 : 0.28;
-
   const generalStyle: CSSObject = {
     background: theme.palette.background.default,
     '&, .cm-editor': {
       height: '100%',
     },
-    '.cm-scroller-holder': {
-      display: 'flex',
-      position: 'relative',
-      flexDirection: 'column',
-      overflow: 'hidden',
-      flex: '1 1',
-    },
-    '.cm-scroller-spacer': {
-      position: 'sticky',
-      flexShrink: 0,
-      zIndex: 300,
-      width: 1,
-      marginRight: -1,
-      pointerEvents: 'none',
-    },
     '.cm-scroller': {
       color: theme.palette.text.secondary,
-      scrollbarWidth: 'none',
-      MsOverflowStyle: 'none',
-      '&::-webkit-scrollbar': {
-        width: 0,
-        height: 0,
-        background: 'transparent',
-      },
-    },
-    '.cm-scroller-track': {
-      position: 'absolute',
-      zIndex: 300,
-      touchAction: 'none',
-    },
-    '.cm-scroller-thumb': {
-      position: 'absolute',
-      background: theme.palette.text.secondary,
-      opacity: scrollerThumbOpacity,
-      transition: theme.transitions.create('opacity', {
-        duration: theme.transitions.duration.shortest,
-      }),
-      touchAction: 'none',
-      WebkitTapHighlightColor: 'transparent',
-      '&:hover': {
-        opacity: 0.75,
-        '@media (hover: none)': {
-          opacity: scrollerThumbOpacity,
-        },
-      },
-      '&.active': {
-        opacity: 1,
-        pointerEvents: 'none',
-        userSelect: 'none',
-      },
-    },
-    '.cm-scroller-track-y, .cm-scroller-thumb-y': {
-      top: 0,
-      right: 0,
-      width: 12,
-    },
-    '.cm-scroller-track-x, .cm-scroller-thumb-x': {
-      left: 0,
-      bottom: 0,
-      height: 12,
-    },
-    '.cm-scroller-track-x': {
-      right: 12,
-    },
-    '.cm-scroller-gutter-decoration': {
-      position: 'absolute',
-      top: 0,
-      bottom: 0,
-      left: 0,
-      width: 0,
-      transition: theme.transitions.create('width', {
-        duration: theme.transitions.duration.shortest,
-      }),
-      ...radialShadowTheme('0 50%', true, false),
-    },
-    '.cm-scroller-top-decoration': {
-      position: 'absolute',
-      top: 0,
-      left: 0,
-      right: 0,
-      height: 0,
-      transition: theme.transitions.create('height', {
-        duration: theme.transitions.duration.shortest,
-      }),
-      ...radialShadowTheme('50% 0', false, true),
     },
     '.cm-gutters': {
       background: theme.palette.background.default,
@@ -162,7 +57,6 @@ export default styled('div', {
       background: 'transparent',
     },
     '.cm-cursor, .cm-cursor-primary': {
-      marginLeft: -1,
       borderLeft: `2px solid ${theme.palette.info.main}`,
     },
     '.cm-selectionBackground': {
@@ -175,7 +69,6 @@ export default styled('div', {
       },
     },
     '.cm-line': {
-      position: 'relative', // For indentation highlights
       padding: '0 12px 0 0px',
     },
   };
@@ -265,13 +158,6 @@ export default styled('div', {
     '.cm-searchMatch-selected': {
       background: theme.palette.highlight.search.selected,
     },
-    '.cm-indentation-marker': {
-      display: 'inline-block',
-      boxShadow: `1px 0 0 ${theme.palette.text.disabled} inset`,
-      '&.active': {
-        boxShadow: `1px 0 0 ${theme.palette.text.primary} inset`,
-      },
-    },
     '.cm-scroller-selection': {
       position: 'absolute',
       right: 0,
@@ -452,11 +338,11 @@ export default styled('div', {
 
   const foldStyle = {
     '.cm-foldGutter': {
-      width: 17,
+      width: 16,
     },
     '.problem-editor-foldMarker': {
       display: 'block',
-      margin: '4px 1px 4px 0',
+      margin: '4px 0 4px 0',
       padding: 0,
       maskImage: svgURL(expandMoreSVG),
       maskSize: '16px 16px',
@@ -467,7 +353,7 @@ export default styled('div', {
       cursor: 'pointer',
       WebkitTapHighlightColor: 'transparent',
       [theme.breakpoints.down('sm')]: {
-        margin: '2px 1px 2px 0',
+        margin: '2px 0 2px 0',
       },
     },
     '.problem-editor-foldMarker-open': {
diff --git a/subprojects/frontend/src/editor/GenerateButton.tsx b/subprojects/frontend/src/editor/GenerateButton.tsx
index 2036fc28..3837ef8e 100644
--- a/subprojects/frontend/src/editor/GenerateButton.tsx
+++ b/subprojects/frontend/src/editor/GenerateButton.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import DangerousOutlinedIcon from '@mui/icons-material/DangerousOutlined';
 import PlayArrowIcon from '@mui/icons-material/PlayArrow';
 import Button from '@mui/material/Button';
diff --git a/subprojects/frontend/src/editor/LintPanelStore.ts b/subprojects/frontend/src/editor/LintPanelStore.ts
index 502f9c59..f81587fa 100644
--- a/subprojects/frontend/src/editor/LintPanelStore.ts
+++ b/subprojects/frontend/src/editor/LintPanelStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { closeLintPanel, openLintPanel } from '@codemirror/lint';
 
 import type EditorStore from './EditorStore';
diff --git a/subprojects/frontend/src/editor/PanelStore.ts b/subprojects/frontend/src/editor/PanelStore.ts
index 4f827280..25ef8b6c 100644
--- a/subprojects/frontend/src/editor/PanelStore.ts
+++ b/subprojects/frontend/src/editor/PanelStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { Command } from '@codemirror/view';
 import { action, makeObservable, observable } from 'mobx';
 
diff --git a/subprojects/frontend/src/editor/SearchPanel.ts b/subprojects/frontend/src/editor/SearchPanel.ts
index c9df41b7..b63d5eed 100644
--- a/subprojects/frontend/src/editor/SearchPanel.ts
+++ b/subprojects/frontend/src/editor/SearchPanel.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   type EditorView,
   type Panel,
diff --git a/subprojects/frontend/src/editor/SearchPanelPortal.tsx b/subprojects/frontend/src/editor/SearchPanelPortal.tsx
index 5cf1c90e..b4b07c74 100644
--- a/subprojects/frontend/src/editor/SearchPanelPortal.tsx
+++ b/subprojects/frontend/src/editor/SearchPanelPortal.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import Portal from '@mui/material/Portal';
 import { observer } from 'mobx-react-lite';
 
diff --git a/subprojects/frontend/src/editor/SearchPanelStore.ts b/subprojects/frontend/src/editor/SearchPanelStore.ts
index 65d595a8..6a97baf1 100644
--- a/subprojects/frontend/src/editor/SearchPanelStore.ts
+++ b/subprojects/frontend/src/editor/SearchPanelStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   closeSearchPanel,
   findNext,
diff --git a/subprojects/frontend/src/editor/SearchToolbar.tsx b/subprojects/frontend/src/editor/SearchToolbar.tsx
index 54f3dba7..4ae7e893 100644
--- a/subprojects/frontend/src/editor/SearchToolbar.tsx
+++ b/subprojects/frontend/src/editor/SearchToolbar.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import CloseIcon from '@mui/icons-material/Close';
 import FindReplaceIcon from '@mui/icons-material/FindReplace';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
diff --git a/subprojects/frontend/src/editor/createEditorState.ts b/subprojects/frontend/src/editor/createEditorState.ts
index ce1efa4f..67b8fb9e 100644
--- a/subprojects/frontend/src/editor/createEditorState.ts
+++ b/subprojects/frontend/src/editor/createEditorState.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   closeBrackets,
   closeBracketsKeymap,
@@ -38,8 +44,6 @@ import type EditorStore from './EditorStore';
 import SearchPanel from './SearchPanel';
 import exposeDiagnostics from './exposeDiagnostics';
 import findOccurrences from './findOccurrences';
-import indentationMarkerViewPlugin from './indentationMarkerViewPlugin';
-import scrollbarViewPlugin from './scrollbarViewPlugin';
 import semanticHighlighting from './semanticHighlighting';
 
 export default function createEditorState(
@@ -64,7 +68,6 @@ export default function createEditorState(
       highlightSpecialChars(),
       history(),
       indentOnInput(),
-      indentationMarkerViewPlugin(),
       rectangularSelection(),
       search({
         createPanel(view) {
@@ -123,7 +126,6 @@ export default function createEditorState(
         ...defaultKeymap,
       ]),
       problemLanguageSupport(),
-      scrollbarViewPlugin(store),
     ],
   });
 }
diff --git a/subprojects/frontend/src/editor/defineDecorationSetExtension.ts b/subprojects/frontend/src/editor/defineDecorationSetExtension.ts
index d9c7bc7d..0887c92e 100644
--- a/subprojects/frontend/src/editor/defineDecorationSetExtension.ts
+++ b/subprojects/frontend/src/editor/defineDecorationSetExtension.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { StateEffect, StateField, TransactionSpec } from '@codemirror/state';
 import { EditorView, Decoration, DecorationSet } from '@codemirror/view';
 
diff --git a/subprojects/frontend/src/editor/exposeDiagnostics.ts b/subprojects/frontend/src/editor/exposeDiagnostics.ts
index 82f24c93..c4dcbb87 100644
--- a/subprojects/frontend/src/editor/exposeDiagnostics.ts
+++ b/subprojects/frontend/src/editor/exposeDiagnostics.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { setDiagnosticsEffect } from '@codemirror/lint';
 import {
   StateField,
diff --git a/subprojects/frontend/src/editor/findOccurrences.ts b/subprojects/frontend/src/editor/findOccurrences.ts
index 08c078c2..00dffc96 100644
--- a/subprojects/frontend/src/editor/findOccurrences.ts
+++ b/subprojects/frontend/src/editor/findOccurrences.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   type Range,
   RangeSet,
diff --git a/subprojects/frontend/src/editor/indentationMarkerViewPlugin.ts b/subprojects/frontend/src/editor/indentationMarkerViewPlugin.ts
deleted file mode 100644
index 730fa6e3..00000000
--- a/subprojects/frontend/src/editor/indentationMarkerViewPlugin.ts
+++ /dev/null
@@ -1,341 +0,0 @@
-/**
- * @file CodeMirror plugin to highlight indentation
- *
- * This file is based on the
- * [@replit/codemirror-indentation-markers](https://github.com/replit/codemirror-indentation-markers)
- * package, which is available under the
- * [MIT License](https://github.com/replit/codemirror-indentation-markers/blob/543cc508ca5cef5d8350af23973eb1425e31525c/LICENSE).
- *
- * The highlighting heuristics were adjusted to make them more suitable
- * for logic programming.
- *
- * @see https://github.com/replit/codemirror-indentation-markers/blob/543cc508ca5cef5d8350af23973eb1425e31525c/src/index.ts
- */
-
-import { getIndentUnit } from '@codemirror/language';
-import { Text, RangeSet, EditorState } from '@codemirror/state';
-import {
-  ViewPlugin,
-  Decoration,
-  EditorView,
-  WidgetType,
-  PluginValue,
-} from '@codemirror/view';
-
-export const INDENTATION_MARKER_CLASS = 'cm-indentation-marker';
-
-export const INDENTATION_MARKER_ACTIVE_CLASS = 'active';
-
-const indentationMark = Decoration.mark({
-  class: INDENTATION_MARKER_CLASS,
-  tagName: 'span',
-});
-
-const activeIndentationMark = Decoration.mark({
-  class: `${INDENTATION_MARKER_CLASS} ${INDENTATION_MARKER_ACTIVE_CLASS}`,
-  tagName: 'span',
-});
-
-/**
- * Widget used to simulate N indentation markers on empty lines.
- */
-class IndentationWidget extends WidgetType {
-  constructor(
-    readonly numIndent: number,
-    readonly indentSize: number,
-    readonly activeIndent?: number,
-  ) {
-    super();
-  }
-
-  override eq(other: IndentationWidget) {
-    return (
-      this.numIndent === other.numIndent &&
-      this.indentSize === other.indentSize &&
-      this.activeIndent === other.activeIndent
-    );
-  }
-
-  override toDOM(view: EditorView) {
-    const indentSize = getIndentUnit(view.state);
-
-    const wrapper = document.createElement('span');
-    wrapper.style.top = '0';
-    wrapper.style.left = '0';
-    wrapper.style.position = 'absolute';
-    wrapper.style.pointerEvents = 'none';
-
-    for (let indent = 0; indent < this.numIndent; indent += 1) {
-      const element = document.createElement('span');
-      element.className = INDENTATION_MARKER_CLASS;
-      element.classList.toggle(
-        INDENTATION_MARKER_ACTIVE_CLASS,
-        indent === this.activeIndent,
-      );
-      element.innerHTML = ' '.repeat(indentSize);
-      wrapper.appendChild(element);
-    }
-
-    return wrapper;
-  }
-}
-
-/**
- * Returns the number of indentation markers a non-empty line should have
- * based on the text in the line and the size of the indent.
- */
-function getNumIndentMarkersForNonEmptyLine(
-  text: string,
-  indentSize: number,
-  onIndentMarker?: (pos: number) => void,
-) {
-  let numIndents = 0;
-  let numConsecutiveSpaces = 0;
-  let prevChar: string | undefined;
-
-  for (let char = 0; char < text.length; char += 1) {
-    // Bail if we encounter a non-whitespace character
-    if (text[char] !== ' ' && text[char] !== '\t') {
-      // We still increment the indentation level if we would
-      // have added a marker here had this been a space or tab.
-      if (numConsecutiveSpaces % indentSize === 0 && char !== 0) {
-        numIndents += 1;
-      }
-
-      return numIndents;
-    }
-
-    // Every tab and N space has an indentation marker
-    const shouldAddIndent =
-      prevChar === '\t' || numConsecutiveSpaces % indentSize === 0;
-
-    if (shouldAddIndent) {
-      numIndents += 1;
-
-      if (onIndentMarker) {
-        onIndentMarker(char);
-      }
-    }
-
-    if (text[char] === ' ') {
-      numConsecutiveSpaces += 1;
-    } else {
-      numConsecutiveSpaces = 0;
-    }
-
-    prevChar = text[char];
-  }
-
-  return numIndents;
-}
-
-/**
- * Returns the number of indent markers an empty line should have
- * based on the number of indent markers of the previous
- * and next non-empty lines.
- */
-function getNumIndentMarkersForEmptyLine(prev: number, next: number) {
-  const min = Math.min(prev, next);
-  const max = Math.max(prev, next);
-
-  // If only one side is non-zero, we omit markers,
-  // because in logic programming, a block often ends with an empty line.
-  if (min === 0 && max > 0) {
-    return 0;
-  }
-
-  // Else, default to the minimum of the two
-  return min;
-}
-
-/**
- * Returns the next non-empty line and its indent level.
- */
-function findNextNonEmptyLineAndIndentLevel(
-  doc: Text,
-  startLine: number,
-  indentSize: number,
-): [number, number] {
-  const numLines = doc.lines;
-  let lineNo = startLine;
-
-  while (lineNo <= numLines) {
-    const { text } = doc.line(lineNo);
-
-    if (text.trim().length === 0) {
-      lineNo += 1;
-    } else {
-      const indent = getNumIndentMarkersForNonEmptyLine(text, indentSize);
-      return [lineNo, indent];
-    }
-  }
-
-  // Reached the end of the doc
-  return [numLines + 1, 0];
-}
-
-interface IndentationMarkerDesc {
-  lineNumber: number;
-  from: number;
-  to: number;
-  create(activeIndentIndex?: number): Decoration;
-}
-
-/**
- * Returns a range of lines with an active indent marker.
- */
-function getLinesWithActiveIndentMarker(
-  state: EditorState,
-  indentMap: Map<number, number>,
-): { start: number; end: number; activeIndent: number } {
-  const currentLine = state.doc.lineAt(state.selection.main.head);
-  const currentIndent = indentMap.get(currentLine.number);
-  const currentLineNo = currentLine.number;
-
-  if (!currentIndent) {
-    return { start: -1, end: -1, activeIndent: NaN };
-  }
-
-  let start: number;
-  let end: number;
-
-  for (start = currentLineNo; start >= 0; start -= 1) {
-    const indent = indentMap.get(start - 1);
-    if (!indent || indent < currentIndent) {
-      break;
-    }
-  }
-
-  for (end = currentLineNo; ; end += 1) {
-    const indent = indentMap.get(end + 1);
-    if (!indent || indent < currentIndent) {
-      break;
-    }
-  }
-
-  return { start, end, activeIndent: currentIndent };
-}
-/**
- * Adds indentation markers to all lines within view.
- */
-function addIndentationMarkers(view: EditorView) {
-  const indentSize = getIndentUnit(view.state);
-  const indentSizeMap = new Map</* lineNumber */ number, number>();
-  const decorations: Array<IndentationMarkerDesc> = [];
-
-  view.visibleRanges.forEach(({ from, to }) => {
-    let pos = from;
-
-    let prevIndentMarkers = 0;
-    let nextIndentMarkers = 0;
-    let nextNonEmptyLine = 0;
-
-    while (pos <= to) {
-      const line = view.state.doc.lineAt(pos);
-      const { text } = line;
-
-      // If a line is empty, we match the indentation according
-      // to a heuristic based on the indentations of the
-      // previous and next non-empty lines.
-      if (text.trim().length === 0) {
-        // To retrieve the next non-empty indentation level,
-        // we perform a lookahead and cache the result.
-        if (nextNonEmptyLine < line.number) {
-          const [nextLine, nextIndent] = findNextNonEmptyLineAndIndentLevel(
-            view.state.doc,
-            line.number + 1,
-            indentSize,
-          );
-
-          nextNonEmptyLine = nextLine;
-          nextIndentMarkers = nextIndent;
-        }
-
-        const numIndentMarkers = getNumIndentMarkersForEmptyLine(
-          prevIndentMarkers,
-          nextIndentMarkers,
-        );
-
-        // Add the indent widget and move on to next line
-        indentSizeMap.set(line.number, numIndentMarkers);
-        decorations.push({
-          from: pos,
-          to: pos,
-          lineNumber: line.number,
-          create: (activeIndentIndex) =>
-            Decoration.widget({
-              widget: new IndentationWidget(
-                numIndentMarkers,
-                indentSize,
-                activeIndentIndex,
-              ),
-            }),
-        });
-      } else {
-        const indices: Array<number> = [];
-
-        prevIndentMarkers = getNumIndentMarkersForNonEmptyLine(
-          text,
-          indentSize,
-          (char) => indices.push(char),
-        );
-
-        indentSizeMap.set(line.number, indices.length);
-        decorations.push(
-          ...indices.map(
-            (char, i): IndentationMarkerDesc => ({
-              from: line.from + char,
-              to: line.from + char + 1,
-              lineNumber: line.number,
-              create: (activeIndentIndex) =>
-                activeIndentIndex === i
-                  ? activeIndentationMark
-                  : indentationMark,
-            }),
-          ),
-        );
-      }
-
-      // Move on to the next line
-      pos = line.to + 1;
-    }
-  });
-
-  const activeBlockRange = getLinesWithActiveIndentMarker(
-    view.state,
-    indentSizeMap,
-  );
-
-  return RangeSet.of<Decoration>(
-    Array.from(decorations).map(({ lineNumber, from, to, create }) => {
-      const activeIndent =
-        lineNumber >= activeBlockRange.start &&
-        lineNumber <= activeBlockRange.end
-          ? activeBlockRange.activeIndent - 1
-          : undefined;
-
-      return { from, to, value: create(activeIndent) };
-    }),
-    true,
-  );
-}
-
-export default function indentationMarkerViewPlugin() {
-  return ViewPlugin.define<PluginValue & { decorations: RangeSet<Decoration> }>(
-    (view) => ({
-      decorations: addIndentationMarkers(view),
-      update(update) {
-        if (
-          update.docChanged ||
-          update.viewportChanged ||
-          update.selectionSet
-        ) {
-          this.decorations = addIndentationMarkers(update.view);
-        }
-      },
-    }),
-    {
-      decorations: (v) => v.decorations,
-    },
-  );
-}
diff --git a/subprojects/frontend/src/editor/scrollbarViewPlugin.ts b/subprojects/frontend/src/editor/scrollbarViewPlugin.ts
deleted file mode 100644
index f54251a9..00000000
--- a/subprojects/frontend/src/editor/scrollbarViewPlugin.ts
+++ /dev/null
@@ -1,358 +0,0 @@
-import { EditorSelection } from '@codemirror/state';
-import {
-  type EditorView,
-  type PluginValue,
-  ViewPlugin,
-} from '@codemirror/view';
-import { reaction } from 'mobx';
-
-import type EditorStore from './EditorStore';
-import { getDiagnostics } from './exposeDiagnostics';
-import findOccurrences from './findOccurrences';
-
-export const HOLDER_CLASS = 'cm-scroller-holder';
-export const SPACER_CLASS = 'cm-scroller-spacer';
-export const TRACK_CLASS = 'cm-scroller-track';
-export const THUMB_CLASS = 'cm-scroller-thumb';
-export const THUMB_ACTIVE_CLASS = 'active';
-export const GUTTER_DECORATION_CLASS = 'cm-scroller-gutter-decoration';
-export const TOP_DECORATION_CLASS = 'cm-scroller-top-decoration';
-export const ANNOTATION_SELECTION_CLASS = 'cm-scroller-selection';
-export const ANNOTATION_DIAGNOSTIC_CLASS = 'cm-scroller-diagnostic';
-export const ANNOTATION_OCCURRENCE_CLASS = 'cm-scroller-occurrence';
-export const SHADOW_WIDTH = 10;
-export const SCROLLBAR_WIDTH = 12;
-export const ANNOTATION_WIDTH = SCROLLBAR_WIDTH / 2;
-export const MIN_ANNOTATION_HEIGHT = 1;
-
-function createScrollbar(
-  holder: HTMLElement,
-  direction: 'x' | 'y',
-  touchCallback: (offsetX: number, offsetY: number) => void,
-  moveCallback: (movementX: number, movementY: number) => void,
-): { track: HTMLElement; thumb: HTMLElement } {
-  const track = holder.ownerDocument.createElement('div');
-  track.className = `${TRACK_CLASS} ${TRACK_CLASS}-${direction}`;
-  holder.appendChild(track);
-
-  const thumb = holder.ownerDocument.createElement('div');
-  thumb.className = `${THUMB_CLASS} ${THUMB_CLASS}-${direction}`;
-  track.appendChild(thumb);
-
-  let pointerId: number | undefined;
-  track.addEventListener('pointerdown', (event) => {
-    if (pointerId !== undefined) {
-      event.preventDefault();
-      return;
-    }
-    ({ pointerId } = event);
-    thumb.classList.add(THUMB_ACTIVE_CLASS);
-    if (event.target === thumb) {
-      // Prevent implicit pointer capture on mobile.
-      thumb.releasePointerCapture(pointerId);
-    } else {
-      touchCallback(event.offsetX, event.offsetY);
-    }
-    track.setPointerCapture(pointerId);
-  });
-
-  track.addEventListener('pointermove', (event) => {
-    if (event.pointerId !== pointerId) {
-      return;
-    }
-    moveCallback(event.movementX, event.movementY);
-    event.preventDefault();
-  });
-
-  function scrollEnd(event: PointerEvent) {
-    if (event.pointerId !== pointerId) {
-      return;
-    }
-    pointerId = undefined;
-    thumb.classList.remove(THUMB_ACTIVE_CLASS);
-  }
-
-  track.addEventListener('pointerup', scrollEnd, { passive: true });
-  track.addEventListener('pointercancel', scrollEnd, { passive: true });
-
-  return { track, thumb };
-}
-
-function rebuildAnnotations(
-  view: EditorView,
-  scrollHeight: number,
-  trackYHeight: number,
-  holder: HTMLElement,
-  annotations: HTMLDivElement[],
-) {
-  const { state } = view;
-  const overlayAnnotationsHeight =
-    (view.contentHeight / scrollHeight) * trackYHeight;
-  const lineHeight = overlayAnnotationsHeight / state.doc.lines;
-
-  let i = 0;
-
-  function getOrCreateAnnotation(from: number, to?: number): HTMLDivElement {
-    const startLine = state.doc.lineAt(from).number;
-    const endLine = to === undefined ? startLine : state.doc.lineAt(to).number;
-    const top = (startLine - 1) * lineHeight;
-    const height = Math.max(
-      MIN_ANNOTATION_HEIGHT,
-      Math.max(1, endLine - startLine) * lineHeight,
-    );
-
-    let annotation: HTMLDivElement | undefined;
-    if (i < annotations.length) {
-      annotation = annotations[i];
-    }
-    if (annotation === undefined) {
-      annotation = holder.ownerDocument.createElement('div');
-      annotations.push(annotation);
-      holder.appendChild(annotation);
-    }
-    i += 1;
-
-    annotation.style.top = `${top}px`;
-    annotation.style.height = `${height}px`;
-
-    return annotation;
-  }
-
-  state.selection.ranges.forEach(({ head }) => {
-    const selectionAnnotation = getOrCreateAnnotation(head);
-    selectionAnnotation.className = ANNOTATION_SELECTION_CLASS;
-    selectionAnnotation.style.width = `${SCROLLBAR_WIDTH}px`;
-  });
-
-  const diagnosticsIter = getDiagnostics(state).iter();
-  while (diagnosticsIter.value !== null) {
-    const diagnosticAnnotation = getOrCreateAnnotation(
-      diagnosticsIter.from,
-      diagnosticsIter.to,
-    );
-    diagnosticAnnotation.className = `${ANNOTATION_DIAGNOSTIC_CLASS} ${ANNOTATION_DIAGNOSTIC_CLASS}-${diagnosticsIter.value.severity}`;
-    diagnosticAnnotation.style.width = `${ANNOTATION_WIDTH}px`;
-    diagnosticsIter.next();
-  }
-
-  const occurrences = view.state.field(findOccurrences);
-  const occurrencesIter = occurrences.iter();
-  while (occurrencesIter.value !== null) {
-    const occurrenceAnnotation = getOrCreateAnnotation(
-      occurrencesIter.from,
-      occurrencesIter.to,
-    );
-    occurrenceAnnotation.className = ANNOTATION_OCCURRENCE_CLASS;
-    occurrenceAnnotation.style.width = `${ANNOTATION_WIDTH}px`;
-    occurrenceAnnotation.style.right = `${ANNOTATION_WIDTH}px`;
-    occurrencesIter.next();
-  }
-
-  annotations
-    .splice(i)
-    .forEach((staleAnnotation) => holder.removeChild(staleAnnotation));
-}
-
-export default function scrollbarViewPlugin(
-  editorStore: EditorStore,
-): ViewPlugin<PluginValue> {
-  return ViewPlugin.define((view) => {
-    const { scrollDOM } = view;
-    const { ownerDocument, parentElement: parentDOM } = scrollDOM;
-    if (parentDOM === null) {
-      return {};
-    }
-
-    const holder = ownerDocument.createElement('div');
-    holder.className = HOLDER_CLASS;
-    parentDOM.replaceChild(holder, scrollDOM);
-    holder.appendChild(scrollDOM);
-
-    const spacer = ownerDocument.createElement('div');
-    spacer.className = SPACER_CLASS;
-    scrollDOM.insertBefore(spacer, scrollDOM.firstChild);
-
-    let gutterWidth = 0;
-
-    scrollDOM.addEventListener('click', (event) => {
-      const scrollX = scrollDOM.scrollLeft + event.offsetX;
-      const scrollY = scrollDOM.scrollTop + event.offsetY;
-      if (scrollX > gutterWidth && scrollY > view.contentHeight) {
-        event.preventDefault();
-        view.focus();
-        editorStore.dispatch({
-          scrollIntoView: true,
-          selection: EditorSelection.create([
-            EditorSelection.cursor(view.state.doc.length),
-          ]),
-        });
-      }
-    });
-
-    let factorY = 1;
-    let factorX = 1;
-
-    const { track: trackY, thumb: thumbY } = createScrollbar(
-      holder,
-      'y',
-      (_offsetX, offsetY) => {
-        const scaledOffset = offsetY / factorY;
-        const { height: scrollerHeight } = scrollDOM.getBoundingClientRect();
-        const target = Math.max(0, scaledOffset - scrollerHeight / 2);
-        scrollDOM.scrollTo({ top: target });
-      },
-      (_movementX, movementY) => {
-        scrollDOM.scrollBy({ top: movementY / factorY });
-      },
-    );
-
-    const { track: trackX, thumb: thumbX } = createScrollbar(
-      holder,
-      'x',
-      (offsetX) => {
-        const scaledOffset = offsetX / factorX;
-        const { width: scrollerWidth } = scrollDOM.getBoundingClientRect();
-        const target = Math.max(0, scaledOffset - scrollerWidth / 2);
-        scrollDOM.scrollTo({ left: target });
-      },
-      (movementX) => {
-        scrollDOM.scrollBy({ left: movementX / factorX });
-      },
-    );
-
-    const gutterDecoration = ownerDocument.createElement('div');
-    gutterDecoration.className = GUTTER_DECORATION_CLASS;
-    holder.appendChild(gutterDecoration);
-
-    const topDecoration = ownerDocument.createElement('div');
-    topDecoration.className = TOP_DECORATION_CLASS;
-    holder.appendChild(topDecoration);
-
-    const disposePanelReaction = reaction(
-      () => editorStore.searchPanel.state,
-      (panelOpen) => {
-        topDecoration.style.display = panelOpen ? 'none' : 'block';
-      },
-      { fireImmediately: true },
-    );
-
-    let gutters: Element | undefined;
-
-    let firstRun = true;
-    let firstRunTimeout: number | undefined;
-    let requested = false;
-    let rebuildRequested = false;
-
-    const annotations: HTMLDivElement[] = [];
-
-    let observer: ResizeObserver | undefined;
-
-    function update() {
-      requested = false;
-
-      if (gutters === undefined) {
-        gutters = scrollDOM.querySelector('.cm-gutters') ?? undefined;
-        if (gutters !== undefined && observer !== undefined) {
-          observer.observe(gutters);
-        }
-      }
-
-      const { height: scrollerHeight, width: scrollerWidth } =
-        scrollDOM.getBoundingClientRect();
-      const { scrollTop, scrollLeft, scrollWidth } = scrollDOM;
-      const scrollHeight =
-        view.contentHeight + scrollerHeight - view.defaultLineHeight;
-      if (firstRun) {
-        if (firstRunTimeout !== undefined) {
-          clearTimeout(firstRunTimeout);
-        }
-        // @ts-expect-error `@types/node` typings should not be in effect here.
-        firstRunTimeout = setTimeout(() => {
-          spacer.style.minHeight = `${scrollHeight}px`;
-          firstRun = false;
-        }, 0);
-      } else {
-        spacer.style.minHeight = `${scrollHeight}px`;
-      }
-      gutterWidth = gutters?.clientWidth ?? 0;
-      let trackYHeight = scrollerHeight;
-
-      // Prevent spurious horizontal scrollbar by rounding up to the nearest pixel.
-      if (scrollWidth > Math.ceil(scrollerWidth)) {
-        // Leave space for horizontal scrollbar.
-        trackYHeight -= SCROLLBAR_WIDTH;
-        // Alwalys leave space for annotation in the vertical scrollbar.
-        const trackXWidth = scrollerWidth - gutterWidth - SCROLLBAR_WIDTH;
-        const thumbWidth = trackXWidth * (scrollerWidth / scrollWidth);
-        factorX = (trackXWidth - thumbWidth) / (scrollWidth - scrollerWidth);
-        trackY.style.bottom = `${SCROLLBAR_WIDTH}px`;
-        trackX.style.display = 'block';
-        trackX.style.left = `${gutterWidth}px`;
-        thumbX.style.width = `${thumbWidth}px`;
-        thumbX.style.left = `${scrollLeft * factorX}px`;
-        scrollDOM.style.overflowX = 'scroll';
-      } else {
-        trackY.style.bottom = '0px';
-        trackX.style.display = 'none';
-        scrollDOM.style.overflowX = 'hidden';
-      }
-
-      const thumbHeight = trackYHeight * (scrollerHeight / scrollHeight);
-      factorY = (trackYHeight - thumbHeight) / (scrollHeight - scrollerHeight);
-      thumbY.style.display = 'block';
-      thumbY.style.height = `${thumbHeight}px`;
-      thumbY.style.top = `${scrollTop * factorY}px`;
-
-      gutterDecoration.style.left = `${gutterWidth}px`;
-      gutterDecoration.style.width = `${Math.max(
-        0,
-        Math.min(scrollLeft, SHADOW_WIDTH),
-      )}px`;
-
-      topDecoration.style.height = `${Math.max(
-        0,
-        Math.min(scrollTop, SHADOW_WIDTH),
-      )}px`;
-
-      if (rebuildRequested) {
-        rebuildAnnotations(
-          view,
-          scrollHeight,
-          trackYHeight,
-          holder,
-          annotations,
-        );
-        rebuildRequested = false;
-      }
-    }
-
-    function requestUpdate() {
-      if (!requested) {
-        requested = true;
-        view.requestMeasure({ read: update });
-      }
-    }
-
-    function requestRebuild() {
-      requestUpdate();
-      rebuildRequested = true;
-    }
-
-    observer = new ResizeObserver(requestRebuild);
-    observer.observe(holder);
-
-    scrollDOM.addEventListener('scroll', requestUpdate);
-
-    requestRebuild();
-
-    return {
-      update: requestRebuild,
-      destroy() {
-        disposePanelReaction();
-        observer?.disconnect();
-        scrollDOM.removeEventListener('scroll', requestUpdate);
-        parentDOM.replaceChild(holder, holder);
-      },
-    };
-  });
-}
diff --git a/subprojects/frontend/src/editor/semanticHighlighting.ts b/subprojects/frontend/src/editor/semanticHighlighting.ts
index 2c1bd67d..1f2e564c 100644
--- a/subprojects/frontend/src/editor/semanticHighlighting.ts
+++ b/subprojects/frontend/src/editor/semanticHighlighting.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { RangeSet, type TransactionSpec } from '@codemirror/state';
 import { Decoration } from '@codemirror/view';
 
diff --git a/subprojects/frontend/src/index.tsx b/subprojects/frontend/src/index.tsx
index 29b2b196..cb11e6c3 100644
--- a/subprojects/frontend/src/index.tsx
+++ b/subprojects/frontend/src/index.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { configure } from 'mobx';
 import { type Root, createRoot } from 'react-dom/client';
 
diff --git a/subprojects/frontend/src/language/folding.ts b/subprojects/frontend/src/language/folding.ts
index 4dabfa27..b4d4ca22 100644
--- a/subprojects/frontend/src/language/folding.ts
+++ b/subprojects/frontend/src/language/folding.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { EditorState } from '@codemirror/state';
 import type { SyntaxNode } from '@lezer/common';
 
diff --git a/subprojects/frontend/src/language/indentation.ts b/subprojects/frontend/src/language/indentation.ts
index a0f7032d..8446d7fa 100644
--- a/subprojects/frontend/src/language/indentation.ts
+++ b/subprojects/frontend/src/language/indentation.ts
@@ -1,3 +1,10 @@
+/*
+ * Copyright (C) 2018-2021 by Marijn Haverbeke <marijnh@gmail.com> and others
+ * Copyright (C) 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+
 import type { TreeIndentContext } from '@codemirror/language';
 
 /**
diff --git a/subprojects/frontend/src/language/problem.grammar b/subprojects/frontend/src/language/problem.grammar
index 704badab..a7b1fb0a 100644
--- a/subprojects/frontend/src/language/problem.grammar
+++ b/subprojects/frontend/src/language/problem.grammar
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 @detectDelim
 
 @external prop implicitCompletion from './props'
diff --git a/subprojects/frontend/src/language/problemLanguageSupport.ts b/subprojects/frontend/src/language/problemLanguageSupport.ts
index c3ae7ed9..2121e05f 100644
--- a/subprojects/frontend/src/language/problemLanguageSupport.ts
+++ b/subprojects/frontend/src/language/problemLanguageSupport.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   foldInside,
   foldNodeProp,
diff --git a/subprojects/frontend/src/language/props.ts b/subprojects/frontend/src/language/props.ts
index 65392e75..aa67145a 100644
--- a/subprojects/frontend/src/language/props.ts
+++ b/subprojects/frontend/src/language/props.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 /* eslint-disable import/prefer-default-export -- Lezer needs non-default exports */
 
 import { NodeProp } from '@lezer/common';
diff --git a/subprojects/frontend/src/theme/ThemeProvider.tsx b/subprojects/frontend/src/theme/ThemeProvider.tsx
index 7bda1ede..78146f25 100644
--- a/subprojects/frontend/src/theme/ThemeProvider.tsx
+++ b/subprojects/frontend/src/theme/ThemeProvider.tsx
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   alpha,
   createTheme,
@@ -6,7 +12,6 @@ import {
   type ThemeOptions,
   ThemeProvider as MaterialUiThemeProvider,
   type TypographyStyle,
-  useTheme,
   type CSSObject,
 } from '@mui/material/styles';
 import { observer } from 'mobx-react-lite';
@@ -70,7 +75,7 @@ function createResponsiveTheme(
     ...options,
     typography: {
       fontFamily:
-        '"InterVariable", "Inter", "Roboto", "Helvetica", "Arial", sans-serif',
+        '"Inter Variable", "Inter", "Roboto", "Helvetica", "Arial", sans-serif',
       fontWeightMedium: 600,
       fontWeightEditorNormal: 400,
       fontWeightEditorBold: 700,
@@ -80,7 +85,7 @@ function createResponsiveTheme(
       },
       editor: {
         fontFamily:
-          '"JetBrains MonoVariable", "JetBrains Mono", "Cascadia Code", "Fira Code", monospace',
+          '"JetBrains Mono Variable", "JetBrains Mono", "Cascadia Code", "Fira Code", monospace',
         fontFeatureSettings: '"liga", "calt"',
         // `rem` for JetBrains MonoVariable make the text too large in Safari.
         fontSize: '16px',
@@ -350,15 +355,14 @@ export function ContrastThemeProvider({
 }: {
   children?: ReactNode;
 }): JSX.Element {
-  const theme = useTheme();
   const contrastTheme = useContext(ContrastThemeContext);
   if (!contrastTheme) {
     throw new Error('ContrastThemeProvider must be used within ThemeProvider');
   }
   return (
-    <ThemeAndContrastThemeProvider theme={contrastTheme} contrastTheme={theme}>
+    <MaterialUiThemeProvider theme={contrastTheme}>
       {children}
-    </ThemeAndContrastThemeProvider>
+    </MaterialUiThemeProvider>
   );
 }
 
@@ -378,7 +382,7 @@ const ThemeProvider = observer(function ThemeProvider({
   return (
     <ThemeAndContrastThemeProvider
       theme={darkMode ? darkTheme : lightTheme}
-      contrastTheme={darkMode ? lightTheme : darkTheme}
+      contrastTheme={darkTheme}
     >
       {children}
     </ThemeAndContrastThemeProvider>
diff --git a/subprojects/frontend/src/theme/ThemeStore.ts b/subprojects/frontend/src/theme/ThemeStore.ts
index e09d8d99..7c657449 100644
--- a/subprojects/frontend/src/theme/ThemeStore.ts
+++ b/subprojects/frontend/src/theme/ThemeStore.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { makeAutoObservable } from 'mobx';
 
 export enum ThemePreference {
diff --git a/subprojects/frontend/src/utils/CancelledError.ts b/subprojects/frontend/src/utils/CancelledError.ts
index ee23676f..96b67af7 100644
--- a/subprojects/frontend/src/utils/CancelledError.ts
+++ b/subprojects/frontend/src/utils/CancelledError.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 export default class CancelledError extends Error {
   constructor(message = 'Operation cancelled') {
     super(message);
diff --git a/subprojects/frontend/src/utils/PendingTask.ts b/subprojects/frontend/src/utils/PendingTask.ts
index fd52cef1..80d1a346 100644
--- a/subprojects/frontend/src/utils/PendingTask.ts
+++ b/subprojects/frontend/src/utils/PendingTask.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import TimeoutError from './TimeoutError';
 import getLogger from './getLogger';
 
@@ -20,7 +26,6 @@ export default class PendingTask<T> {
   ) {
     this.resolveCallback = resolveCallback;
     this.rejectCallback = rejectCallback;
-    // @ts-expect-error See https://github.com/mobxjs/mobx/issues/3582 on `@types/node` pollution
     this.timeout = setTimeout(() => {
       if (!this.resolved) {
         this.reject(new TimeoutError());
diff --git a/subprojects/frontend/src/utils/PriorityMutex.ts b/subprojects/frontend/src/utils/PriorityMutex.ts
index 78736141..c1215c76 100644
--- a/subprojects/frontend/src/utils/PriorityMutex.ts
+++ b/subprojects/frontend/src/utils/PriorityMutex.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import CancelledError from './CancelledError';
 import PendingTask from './PendingTask';
 import getLogger from './getLogger';
diff --git a/subprojects/frontend/src/utils/TimeoutError.ts b/subprojects/frontend/src/utils/TimeoutError.ts
index eb800f40..21365502 100644
--- a/subprojects/frontend/src/utils/TimeoutError.ts
+++ b/subprojects/frontend/src/utils/TimeoutError.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 export default class TimeoutError extends Error {
   constructor() {
     super('Operation timed out');
diff --git a/subprojects/frontend/src/utils/getLogger.ts b/subprojects/frontend/src/utils/getLogger.ts
index 301fd76d..09b0b17f 100644
--- a/subprojects/frontend/src/utils/getLogger.ts
+++ b/subprojects/frontend/src/utils/getLogger.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import styles, { type CSPair } from 'ansi-styles';
 import log from 'loglevel';
 import prefix from 'loglevel-plugin-prefix';
diff --git a/subprojects/frontend/src/utils/useDelayedSnackbar.ts b/subprojects/frontend/src/utils/useDelayedSnackbar.ts
index 54716c0c..3d6df3e3 100644
--- a/subprojects/frontend/src/utils/useDelayedSnackbar.ts
+++ b/subprojects/frontend/src/utils/useDelayedSnackbar.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   useSnackbar,
   type SnackbarKey,
@@ -21,7 +27,6 @@ export default function useDelayedSnackbar(
       delay = defaultDelay,
     ) => {
       let key: SnackbarKey | undefined;
-      // @ts-expect-error See https://github.com/mobxjs/mobx/issues/3582 on `@types/node` pollution
       let timeout: number | undefined = setTimeout(() => {
         timeout = undefined;
         key = enqueueSnackbar(message, options);
diff --git a/subprojects/frontend/src/xtext/BackendConfig.ts b/subprojects/frontend/src/xtext/BackendConfig.ts
index 41737c0b..4c7eac5f 100644
--- a/subprojects/frontend/src/xtext/BackendConfig.ts
+++ b/subprojects/frontend/src/xtext/BackendConfig.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 /* eslint-disable @typescript-eslint/no-redeclare -- Declare types with their companion objects */
 
 import { z } from 'zod';
diff --git a/subprojects/frontend/src/xtext/ContentAssistService.ts b/subprojects/frontend/src/xtext/ContentAssistService.ts
index 78f61c06..fd30c4f9 100644
--- a/subprojects/frontend/src/xtext/ContentAssistService.ts
+++ b/subprojects/frontend/src/xtext/ContentAssistService.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type {
   Completion,
   CompletionContext,
diff --git a/subprojects/frontend/src/xtext/HighlightingService.ts b/subprojects/frontend/src/xtext/HighlightingService.ts
index a126ee40..447f1401 100644
--- a/subprojects/frontend/src/xtext/HighlightingService.ts
+++ b/subprojects/frontend/src/xtext/HighlightingService.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type EditorStore from '../editor/EditorStore';
 import type { IHighlightRange } from '../editor/semanticHighlighting';
 
diff --git a/subprojects/frontend/src/xtext/OccurrencesService.ts b/subprojects/frontend/src/xtext/OccurrencesService.ts
index fc72ead2..c9c6c699 100644
--- a/subprojects/frontend/src/xtext/OccurrencesService.ts
+++ b/subprojects/frontend/src/xtext/OccurrencesService.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { Transaction } from '@codemirror/state';
 import { debounce } from 'lodash-es';
 import ms from 'ms';
diff --git a/subprojects/frontend/src/xtext/UpdateService.ts b/subprojects/frontend/src/xtext/UpdateService.ts
index 63e28652..ee5ebde2 100644
--- a/subprojects/frontend/src/xtext/UpdateService.ts
+++ b/subprojects/frontend/src/xtext/UpdateService.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { ChangeDesc, Transaction } from '@codemirror/state';
 import { debounce } from 'lodash-es';
 import { nanoid } from 'nanoid';
diff --git a/subprojects/frontend/src/xtext/UpdateStateTracker.ts b/subprojects/frontend/src/xtext/UpdateStateTracker.ts
index 5d4ce49e..4ce93ed6 100644
--- a/subprojects/frontend/src/xtext/UpdateStateTracker.ts
+++ b/subprojects/frontend/src/xtext/UpdateStateTracker.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import {
   type ChangeDesc,
   ChangeSet,
diff --git a/subprojects/frontend/src/xtext/ValidationService.ts b/subprojects/frontend/src/xtext/ValidationService.ts
index 72414590..64fb63eb 100644
--- a/subprojects/frontend/src/xtext/ValidationService.ts
+++ b/subprojects/frontend/src/xtext/ValidationService.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type { Diagnostic } from '@codemirror/lint';
 
 import type EditorStore from '../editor/EditorStore';
diff --git a/subprojects/frontend/src/xtext/XtextClient.ts b/subprojects/frontend/src/xtext/XtextClient.ts
index 14fb2430..e8181af0 100644
--- a/subprojects/frontend/src/xtext/XtextClient.ts
+++ b/subprojects/frontend/src/xtext/XtextClient.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import type {
   CompletionContext,
   CompletionResult,
diff --git a/subprojects/frontend/src/xtext/XtextWebSocketClient.ts b/subprojects/frontend/src/xtext/XtextWebSocketClient.ts
index 6b734546..6bb7eec8 100644
--- a/subprojects/frontend/src/xtext/XtextWebSocketClient.ts
+++ b/subprojects/frontend/src/xtext/XtextWebSocketClient.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import { createAtom, makeAutoObservable, observable } from 'mobx';
 import ms from 'ms';
 import { nanoid } from 'nanoid';
diff --git a/subprojects/frontend/src/xtext/fetchBackendConfig.ts b/subprojects/frontend/src/xtext/fetchBackendConfig.ts
index 15e976d8..71ff2e63 100644
--- a/subprojects/frontend/src/xtext/fetchBackendConfig.ts
+++ b/subprojects/frontend/src/xtext/fetchBackendConfig.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import BackendConfig, { ENDPOINT } from './BackendConfig';
 
 export default async function fetchBackendConfig(): Promise<BackendConfig> {
diff --git a/subprojects/frontend/src/xtext/webSocketMachine.ts b/subprojects/frontend/src/xtext/webSocketMachine.ts
index 216ed86a..2fb1f52f 100644
--- a/subprojects/frontend/src/xtext/webSocketMachine.ts
+++ b/subprojects/frontend/src/xtext/webSocketMachine.ts
@@ -1,5 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import ms from 'ms';
-import { actions, assign, createMachine, RaiseAction } from 'xstate';
+import { actions, assign, createMachine } from 'xstate';
 
 const { raise } = actions;
 
@@ -217,16 +223,15 @@ export default createMachine(
         ...context,
         errors: [],
       })),
-      // Workaround from https://github.com/statelyai/xstate/issues/1414#issuecomment-699972485
       raiseTimeoutError: raise({
         type: 'ERROR',
         message: 'Open timeout',
-      }) as RaiseAction<WebSocketEvent>,
+      }),
       raisePromiseRejectionError: (_context, { data }) =>
-        raise({
+        raise<WebSocketContext, WebSocketEvent>({
           type: 'ERROR',
-          message: data,
-        }) as RaiseAction<WebSocketEvent>,
+          message: String(data),
+        }),
     },
   },
 );
diff --git a/subprojects/frontend/src/xtext/xtextMessages.ts b/subprojects/frontend/src/xtext/xtextMessages.ts
index ec7a2a31..bbbff064 100644
--- a/subprojects/frontend/src/xtext/xtextMessages.ts
+++ b/subprojects/frontend/src/xtext/xtextMessages.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 /* eslint-disable @typescript-eslint/no-redeclare -- Declare types with their companion objects */
 
 import { z } from 'zod';
diff --git a/subprojects/frontend/src/xtext/xtextServiceResults.ts b/subprojects/frontend/src/xtext/xtextServiceResults.ts
index e93c6714..d3b467ad 100644
--- a/subprojects/frontend/src/xtext/xtextServiceResults.ts
+++ b/subprojects/frontend/src/xtext/xtextServiceResults.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 /* eslint-disable @typescript-eslint/no-redeclare -- Declare types with their companion objects */
 
 import { z } from 'zod';
diff --git a/subprojects/frontend/tsconfig.base.json b/subprojects/frontend/tsconfig.base.json
index 585866f1..5ef50b5e 100644
--- a/subprojects/frontend/tsconfig.base.json
+++ b/subprojects/frontend/tsconfig.base.json
@@ -1,7 +1,41 @@
+/*
+ * Copyright (c) Microsoft Corporation.
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ *
+ * This file is based on
+ * https://github.com/tsconfig/bases/blob/7db25a41bc5a9c0f66d91f6f3aa28438afcb2f18/bases/strictest.json
+ * but we moved it inside the project for better tooling support.
+ */
 {
-  "extends": "@tsconfig/node18-strictest-esm/tsconfig.json",
   "compilerOptions": {
-    "useDefineForClassFields": true,
+    "strict": true,
+    "allowUnusedLabels": false,
+    "allowUnreachableCode": false,
+    "exactOptionalPropertyTypes": true,
+    "noFallthroughCasesInSwitch": true,
+    "noImplicitOverride": true,
+    "noImplicitReturns": true,
+    "noPropertyAccessFromIndexSignature": true,
+    "noUncheckedIndexedAccess": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    // "verbatimModuleSyntax" is incompatible with `import` syntax in modules
+    // with CommonJS import resolution, so we use "isolatedModules" only.
+    // "verbatimModuleSyntax": false,
     "isolatedModules": true,
+    "checkJs": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "forceConsistentCasingInFileNames": true,
+    "useDefineForClassFields": true,
+    // Project-specific configuration below.
+    "module": "es2022",
+    "moduleResolution": "node",
+    "incremental": true,
+    "declaration": true,
+    "emitDeclarationOnly": true,
+    "outDir": "build/typescript"
   }
 }
diff --git a/subprojects/frontend/tsconfig.json b/subprojects/frontend/tsconfig.json
index 35abd789..06f6d8fe 100644
--- a/subprojects/frontend/tsconfig.json
+++ b/subprojects/frontend/tsconfig.json
@@ -1,8 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 {
   "extends": "./tsconfig.base.json",
   "compilerOptions": {
     "jsx": "react-jsx",
-    "noEmit": true,
     "lib": ["DOM", "DOM.Iterable", "ES2022"],
     "types": ["vite/client", "vite-plugin-pwa/client"]
   },
diff --git a/subprojects/frontend/tsconfig.node.json b/subprojects/frontend/tsconfig.node.json
index f4908bcb..47feaf97 100644
--- a/subprojects/frontend/tsconfig.node.json
+++ b/subprojects/frontend/tsconfig.node.json
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 {
   "extends": "./tsconfig.base.json",
   "compilerOptions": {
@@ -10,6 +15,7 @@
   "include": [
     ".eslintrc.cjs",
     "config/*.ts",
+    "config/*.cjs",
     "prettier.config.cjs",
     "types/node",
     "vite.config.ts"
diff --git a/subprojects/frontend/tsconfig.shared.json b/subprojects/frontend/tsconfig.shared.json
index b7e1de55..154fe122 100644
--- a/subprojects/frontend/tsconfig.shared.json
+++ b/subprojects/frontend/tsconfig.shared.json
@@ -1,13 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 {
   "extends": "./tsconfig.base.json",
   "compilerOptions": {
     "composite": true,
     "lib": ["ES2022"],
     "types": [],
-    "emitDeclarationOnly": true,
-    "outDir": "build/typescript"
   },
   "include": [
-    "src/xtext/BackendConfig.ts",
+    "src/xtext/BackendConfig.ts"
   ]
 }
diff --git a/subprojects/frontend/types/ImportMeta.d.ts b/subprojects/frontend/types/ImportMeta.d.ts
index c32b48f5..f5a32ef1 100644
--- a/subprojects/frontend/types/ImportMeta.d.ts
+++ b/subprojects/frontend/types/ImportMeta.d.ts
@@ -1,3 +1,10 @@
+/*
+ * Copyright (c) 2019-present, Yuxi (Evan) You and Vite contributors
+ * Copyright (c) 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+
 interface ImportMeta {
   env: {
     BASE_URL: string;
diff --git a/subprojects/frontend/types/grammar.d.ts b/subprojects/frontend/types/grammar.d.ts
index 1480085b..e7a7eebf 100644
--- a/subprojects/frontend/types/grammar.d.ts
+++ b/subprojects/frontend/types/grammar.d.ts
@@ -1,3 +1,10 @@
+/*
+ * Copyright (C) 2018 by Marijn Haverbeke <marijn@haverbeke.berlin> and others
+ * Copyright (C) 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+
 declare module '*.grammar' {
   import type { LRParser } from '@lezer/lr';
 
diff --git a/subprojects/frontend/types/node/@lezer-generator-rollup.d.ts b/subprojects/frontend/types/node/@lezer-generator-rollup.d.ts
index 9c1ff03e..4ef9f4e3 100644
--- a/subprojects/frontend/types/node/@lezer-generator-rollup.d.ts
+++ b/subprojects/frontend/types/node/@lezer-generator-rollup.d.ts
@@ -1,3 +1,10 @@
+/*
+ * Copyright (C) 2018 by Marijn Haverbeke <marijn@haverbeke.berlin> and others
+ * Copyright (C) 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+
 // We have to explicitly redeclare the type of the `./rollup` ESM export of `@lezer/generator`,
 // because TypeScript can't find it on its own even with `"moduleResolution": "Node16"`.
 declare module '@lezer/generator/rollup' {
diff --git a/subprojects/frontend/types/windowControlsOverlay.d.ts b/subprojects/frontend/types/windowControlsOverlay.d.ts
index d8f3182f..2513d620 100644
--- a/subprojects/frontend/types/windowControlsOverlay.d.ts
+++ b/subprojects/frontend/types/windowControlsOverlay.d.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 interface WindowControlsOverlayGeometryChangeEvent extends Event {
   titlebarAreaRect: DOMRect;
 
diff --git a/subprojects/frontend/vite.config.ts b/subprojects/frontend/vite.config.ts
index cd9993cc..9e08ccc4 100644
--- a/subprojects/frontend/vite.config.ts
+++ b/subprojects/frontend/vite.config.ts
@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
 
diff --git a/subprojects/language-ide/build.gradle b/subprojects/language-ide/build.gradle
deleted file mode 100644
index 3786762b..00000000
--- a/subprojects/language-ide/build.gradle
+++ /dev/null
@@ -1,18 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-        id 'refinery-xtext-conventions'
-}
-
-dependencies {
-        api project(':refinery-language')
-        api libs.xtext.ide
-        api libs.xtext.xbase.ide
-}
-
-def generateXtextLanguage = project(':refinery-language').tasks.named('generateXtextLanguage')
-
-for (taskName in ['compileJava', 'processResources']) {
-        tasks.named(taskName) {
-                dependsOn generateXtextLanguage
-        }
-}
diff --git a/subprojects/language-ide/build.gradle.kts b/subprojects/language-ide/build.gradle.kts
new file mode 100644
index 00000000..1259cd67
--- /dev/null
+++ b/subprojects/language-ide/build.gradle.kts
@@ -0,0 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+        id("tools.refinery.gradle.xtext-generated")
+}
+
+dependencies {
+        api(project(":refinery-language"))
+        api(libs.xtext.ide)
+        api(libs.xtext.xbase.ide)
+        xtextGenerated(project(":refinery-language", "generatedIdeSources"))
+}
+
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeModule.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeModule.java
index fb620065..122fe874 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeModule.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeModule.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.ide;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeSetup.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeSetup.java
index 5b88d41f..9d77e022 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeSetup.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/ProblemIdeSetup.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.ide;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/FuzzyMatcher.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/FuzzyMatcher.java
index fe722ca1..4511223b 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/FuzzyMatcher.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/FuzzyMatcher.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.ide.contentassist;
 
 import org.eclipse.xtext.ide.editor.contentassist.IPrefixMatcher;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/ProblemCrossrefProposalProvider.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/ProblemCrossrefProposalProvider.java
index 8f04ed00..e194ee31 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/ProblemCrossrefProposalProvider.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/ProblemCrossrefProposalProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.ide.contentassist;
 
 import java.util.Objects;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingPartialProblemContentAssistParser.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingPartialProblemContentAssistParser.java
index 3ece6f67..146bd8da 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingPartialProblemContentAssistParser.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingPartialProblemContentAssistParser.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.ide.contentassist;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingProblemParser.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingProblemParser.java
index 80dfee5c..f906d881 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingProblemParser.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/TokenSourceInjectingProblemParser.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.ide.contentassist;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/antlr/ProblemTokenSource.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/antlr/ProblemTokenSource.java
index c6c7f41f..fdc17c4f 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/antlr/ProblemTokenSource.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/contentassist/antlr/ProblemTokenSource.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.29.0.M2
  */
 package tools.refinery.language.ide.contentassist.antlr;
diff --git a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/syntaxcoloring/ProblemSemanticHighlightingCalculator.java b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/syntaxcoloring/ProblemSemanticHighlightingCalculator.java
index 7703e4e3..e8f97d51 100644
--- a/subprojects/language-ide/src/main/java/tools/refinery/language/ide/syntaxcoloring/ProblemSemanticHighlightingCalculator.java
+++ b/subprojects/language-ide/src/main/java/tools/refinery/language/ide/syntaxcoloring/ProblemSemanticHighlightingCalculator.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.ide.syntaxcoloring;
 
 import com.google.common.collect.ImmutableList;
diff --git a/subprojects/language-model/META-INF/MANIFEST.MF b/subprojects/language-model/META-INF/MANIFEST.MF
index a9c6340a..5d36a475 100644
--- a/subprojects/language-model/META-INF/MANIFEST.MF
+++ b/subprojects/language-model/META-INF/MANIFEST.MF
@@ -7,7 +7,7 @@ Bundle-Version: 0.0.0.qualifier
 Bundle-ClassPath: .
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
-Bundle-RequiredExecutionEnvironment: JavaSE-17
+Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Export-Package: tools.refinery.language.model,
  tools.refinery.language.model.problem,
  tools.refinery.language.model.problem.impl,
diff --git a/subprojects/language-model/META-INF/MANIFEST.MF.license b/subprojects/language-model/META-INF/MANIFEST.MF.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/language-model/META-INF/MANIFEST.MF.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/language-model/build.gradle b/subprojects/language-model/build.gradle
deleted file mode 100644
index 275db188..00000000
--- a/subprojects/language-model/build.gradle
+++ /dev/null
@@ -1,55 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-        id 'refinery-mwe2'
-        id 'refinery-sonarqube'
-}
-
-dependencies {
-        api libs.ecore
-        api libs.ecore.xmi
-        mwe2 libs.ecore.codegen
-        mwe2 libs.mwe.utils
-        mwe2 libs.mwe2.lib
-        mwe2 libs.xtext.core
-        mwe2 libs.xtext.xbase
-}
-
-sourceSets {
-        main {
-                java.srcDirs += ['src/main/emf-gen']
-        }
-}
-
-def generateEPackage = tasks.register('generateEPackage', JavaExec) {
-        mainClass = 'org.eclipse.emf.mwe2.launch.runtime.Mwe2Launcher'
-        classpath = configurations.mwe2
-        inputs.file 'src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2'
-        inputs.file 'src/main/resources/model/problem.ecore'
-        inputs.file 'src/main/resources/model/problem.genmodel'
-        outputs.dir 'src/main/emf-gen'
-        args += 'src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2'
-        args += '-p'
-        args += "rootPath=/${projectDir}"
-}
-
-for (taskName in ['compileJava', 'processResources', 'generateEclipseSourceFolders']) {
-        tasks.named(taskName) {
-                dependsOn generateEPackage
-        }
-}
-
-tasks.named('clean') {
-        delete 'src/main/emf-gen'
-}
-
-sonarqube.properties {
-        properties['sonar.exclusions'] += [
-                'src/main/emf-gen/**',
-        ]
-}
-
-eclipse.project.natures += [
-        'org.eclipse.sirius.nature.modelingproject',
-        'org.eclipse.pde.PluginNature',
-        'org.eclipse.xtext.ui.shared.xtextNature'
-]
diff --git a/subprojects/language-model/build.gradle.kts b/subprojects/language-model/build.gradle.kts
new file mode 100644
index 00000000..59ff9046
--- /dev/null
+++ b/subprojects/language-model/build.gradle.kts
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+import tools.refinery.gradle.utils.SonarPropertiesUtils
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+        id("tools.refinery.gradle.mwe2")
+        id("tools.refinery.gradle.sonarqube")
+}
+
+dependencies {
+        api(libs.ecore)
+        api(libs.ecore.xmi)
+        mwe2(libs.ecore.codegen)
+        mwe2(libs.mwe.utils)
+        mwe2(libs.mwe2.lib)
+        mwe2(libs.xtext.core)
+        mwe2(libs.xtext.xbase)
+}
+
+sourceSets {
+        main {
+                java.srcDir("src/main/emf-gen")
+        }
+}
+
+tasks {
+        val generateEPackage by registering(JavaExec::class) {
+                mainClass.set("org.eclipse.emf.mwe2.launch.runtime.Mwe2Launcher")
+                classpath(configurations.mwe2)
+                inputs.file("src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2")
+                inputs.file("src/main/resources/model/problem.ecore")
+                inputs.file("src/main/resources/model/problem.genmodel")
+                outputs.file("build.properties")
+                outputs.file("META-INF/MANIFEST.MF")
+                outputs.file("plugin.xml")
+                outputs.file("plugin.properties")
+                outputs.dir("src/main/emf-gen")
+                args("src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2", "-p", "rootPath=/$projectDir")
+        }
+
+        for (taskName in listOf("compileJava", "processResources", "generateEclipseSourceFolders")) {
+                named(taskName) {
+                        dependsOn(generateEPackage)
+                }
+        }
+
+        clean {
+                delete("src/main/emf-gen")
+        }
+}
+
+sonarqube.properties {
+        SonarPropertiesUtils.addToList(properties, "sonar.exclusions", "src/main/emf-gen/**")
+}
+
+eclipse.project.natures.plusAssign(listOf(
+                "org.eclipse.sirius.nature.modelingproject",
+                "org.eclipse.pde.PluginNature",
+                "org.eclipse.xtext.ui.shared.xtextNature",
+))
diff --git a/subprojects/language-model/build.properties b/subprojects/language-model/build.properties
index 65dfc7c4..9b9859ff 100644
--- a/subprojects/language-model/build.properties
+++ b/subprojects/language-model/build.properties
@@ -1,4 +1,6 @@
+# SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
 #
+# SPDX-License-Identifier: EPL-2.0
 
 bin.includes = .,\
                src/main/resources/model/,\
diff --git a/subprojects/language-model/plugin.properties b/subprojects/language-model/plugin.properties
index c4fb7e23..c410feb7 100644
--- a/subprojects/language-model/plugin.properties
+++ b/subprojects/language-model/plugin.properties
@@ -1,4 +1,6 @@
+# SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
 #
+# SPDX-License-Identifier: EPL-2.0
 
 pluginName = tools.refinery.language.model
 providerName = refinery.tools
diff --git a/subprojects/language-model/plugin.xml b/subprojects/language-model/plugin.xml
index 4ca005a8..ef1e21f4 100644
--- a/subprojects/language-model/plugin.xml
+++ b/subprojects/language-model/plugin.xml
@@ -2,6 +2,9 @@
 <?eclipse version="3.0"?>
 
 <!--
+  SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+  SPDX-License-Identifier: EPL-2.0
 -->
 
 <plugin>
diff --git a/subprojects/language-model/problem.aird.license b/subprojects/language-model/problem.aird.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/language-model/problem.aird.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/language-model/src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2 b/subprojects/language-model/src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2
index 15198d69..074b6b71 100644
--- a/subprojects/language-model/src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2
+++ b/subprojects/language-model/src/main/java/tools/refinery/language/model/GenerateProblemModel.mwe2
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 module tools.refinery.language.model.GenerateProblemModel
 
 Workflow {
diff --git a/subprojects/language-model/src/main/resources/model/problem.ecore.license b/subprojects/language-model/src/main/resources/model/problem.ecore.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/language-model/src/main/resources/model/problem.ecore.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/language-model/src/main/resources/model/problem.genmodel.license b/subprojects/language-model/src/main/resources/model/problem.genmodel.license
new file mode 100644
index 00000000..e5db6ccd
--- /dev/null
+++ b/subprojects/language-model/src/main/resources/model/problem.genmodel.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+
+SPDX-License-Identifier: EPL-2.0
diff --git a/subprojects/language-semantics/build.gradle b/subprojects/language-semantics/build.gradle
deleted file mode 100644
index 4f43ad24..00000000
--- a/subprojects/language-semantics/build.gradle
+++ /dev/null
@@ -1,11 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-}
-
-dependencies {
-        implementation libs.eclipseCollections
-        implementation libs.eclipseCollections.api
-        api project(':refinery-language')
-        api project(':refinery-store')
-        testImplementation testFixtures(project(':refinery-language'))
-}
diff --git a/subprojects/language-semantics/build.gradle.kts b/subprojects/language-semantics/build.gradle.kts
new file mode 100644
index 00000000..38cd9e0d
--- /dev/null
+++ b/subprojects/language-semantics/build.gradle.kts
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+}
+
+dependencies {
+        implementation(libs.eclipseCollections)
+        implementation(libs.eclipseCollections.api)
+        api(project(":refinery-language"))
+        api(project(":refinery-store"))
+        testImplementation(testFixtures(project(":refinery-language")))
+}
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/ModelInitializer.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/ModelInitializer.java
index a6712a89..06b8ad77 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/ModelInitializer.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/ModelInitializer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model;
 
 import com.google.inject.Inject;
@@ -39,8 +44,8 @@ public class ModelInitializer {
                         var isEqualsRelation = relation == builtinSymbols.equals();
                         var decisionTree = mergeAssertions(relationInfo, isEqualsRelation);
                         var defaultValue = isEqualsRelation ? TruthValue.FALSE : TruthValue.UNKNOWN;
-                        relationTrace.put(relation, new Symbol<>(relationInfo.name(), relationInfo.arity(), TruthValue.class, defaultValue
-                        ));
+                        relationTrace.put(relation, Symbol.of(
+                                        relationInfo.name(), relationInfo.arity(), TruthValue.class, defaultValue));
                 }
         }
 
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTree.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTree.java
index 55edee6d..c1afecf9 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTree.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTree.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import org.eclipse.collections.api.factory.primitive.IntObjectMaps;
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeCursor.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeCursor.java
index fdf8e452..9a1e15a3 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeCursor.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeCursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import tools.refinery.store.map.Cursor;
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeNode.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeNode.java
index b81ea3fe..3c54e3c5 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeNode.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeNode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import org.eclipse.collections.api.LazyIntIterable;
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeValue.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeValue.java
index 495a53dd..915ae2bf 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeValue.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/DecisionTreeValue.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import tools.refinery.store.representation.TruthValue;
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/IntermediateNode.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/IntermediateNode.java
index c4200509..e6f01d48 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/IntermediateNode.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/IntermediateNode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import org.eclipse.collections.api.LazyIntIterable;
diff --git a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/TerminalNode.java b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/TerminalNode.java
index 4af836ff..ce49aa62 100644
--- a/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/TerminalNode.java
+++ b/subprojects/language-semantics/src/main/java/tools/refinery/language/semantics/model/internal/TerminalNode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.internal;
 
 import org.eclipse.collections.api.LazyIntIterable;
diff --git a/subprojects/language-semantics/src/test/java/tools/refinery/language/semantics/model/tests/DecisionTreeTests.java b/subprojects/language-semantics/src/test/java/tools/refinery/language/semantics/model/tests/DecisionTreeTests.java
index 4630bf53..b3fcbabb 100644
--- a/subprojects/language-semantics/src/test/java/tools/refinery/language/semantics/model/tests/DecisionTreeTests.java
+++ b/subprojects/language-semantics/src/test/java/tools/refinery/language/semantics/model/tests/DecisionTreeTests.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.semantics.model.tests;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/language-web/build.gradle b/subprojects/language-web/build.gradle
deleted file mode 100644
index 8d277a5b..00000000
--- a/subprojects/language-web/build.gradle
+++ /dev/null
@@ -1,87 +0,0 @@
-plugins {
-        id 'refinery-java-application'
-        id 'refinery-xtext-conventions'
-}
-
-configurations {
-        webapp {
-                canBeConsumed = false
-                canBeResolved = true
-        }
-
-        all {
-                // Use log4j-over-slf4j instead of log4j 1.x
-                exclude group: 'log4j', module: 'log4j'
-        }
-}
-
-dependencies {
-        implementation project(':refinery-language')
-        implementation project(':refinery-language-ide')
-        implementation libs.jetty.server
-        implementation libs.jetty.servlet
-        implementation libs.jetty.websocket.server
-        implementation libs.slf4j.api
-        implementation libs.slf4j.simple
-        implementation libs.slf4j.log4j
-        implementation libs.xtext.web
-        webapp project(path: ':refinery-frontend', configuration: 'productionAssets')
-        testImplementation testFixtures(project(':refinery-language'))
-        testImplementation libs.jetty.websocket.client
-}
-
-def generateXtextLanguage = project(':refinery-language').tasks.named('generateXtextLanguage')
-
-for (taskName in ['compileJava', 'processResources']) {
-        tasks.named(taskName) {
-                dependsOn generateXtextLanguage
-        }
-}
-
-mainClassName = 'tools.refinery.language.web.ServerLauncher'
-
-// Enable JDK 19 preview features for virtual thread support.
-application {
-        applicationDefaultJvmArgs += '--enable-preview'
-}
-tasks.withType(JavaCompile) {
-        options.release = 19
-        options.compilerArgs += '--enable-preview'
-}
-tasks.withType(Test) {
-        jvmArgs += '--enable-preview'
-}
-
-tasks.named('jar') {
-        dependsOn project.configurations.webapp
-        from(project.configurations.webapp) {
-                into 'webapp'
-        }
-}
-
-tasks.named('shadowJar') {
-        dependsOn project.configurations.webapp
-        from(project.sourceSets.main.output)
-        configurations = [project.configurations.runtimeClasspath]
-        exclude('META-INF/INDEX.LIST', 'META-INF/*.SF', 'META-INF/*.DSA', 'META-INF/*.RSA','schema/*',
-                '.options', '.api_description', '*.profile', 'about.*', 'about_*.html', 'about_files/*',
-                'plugin.xml', 'systembundle.properties', 'profile.list', 'META-INF/resources/xtext/**')
-        append('plugin.properties')
-        from(project.configurations.webapp) {
-                into 'webapp'
-        }
-}
-
-tasks.register('serveBackend', JavaExec) {
-        dependsOn project.configurations.webapp
-        dependsOn sourceSets.main.runtimeClasspath
-        classpath = sourceSets.main.runtimeClasspath
-        mainClass = mainClassName
-        // Enable JDK 19 preview features for virtual thread support.
-        jvmArgs += '--enable-preview'
-        standardInput = System.in
-        def baseResource = project.configurations.webapp.incoming.artifacts.artifactFiles.first()
-        environment BASE_RESOURCE: baseResource
-        group = 'run'
-        description = 'Start a Jetty web server serving the Xtex API and assets.'
-}
diff --git a/subprojects/language-web/build.gradle.kts b/subprojects/language-web/build.gradle.kts
new file mode 100644
index 00000000..562a1bd9
--- /dev/null
+++ b/subprojects/language-web/build.gradle.kts
@@ -0,0 +1,68 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-application")
+        id("tools.refinery.gradle.xtext-generated")
+}
+
+val webapp: Configuration by configurations.creating {
+        isCanBeConsumed = false
+        isCanBeResolved = true
+}
+
+dependencies {
+        implementation(project(":refinery-language"))
+        implementation(project(":refinery-language-ide"))
+        implementation(libs.jetty.server)
+        implementation(libs.jetty.servlet)
+        implementation(libs.jetty.websocket.api)
+        implementation(libs.jetty.websocket.server)
+        implementation(libs.slf4j.api)
+        implementation(libs.xtext.web)
+        xtextGenerated(project(":refinery-language", "generatedWebSources"))
+        webapp(project(":refinery-frontend", "productionAssets"))
+        testImplementation(testFixtures(project(":refinery-language")))
+        testImplementation(libs.jetty.websocket.client)
+}
+
+application {
+        mainClass.set("tools.refinery.language.web.ServerLauncher")
+}
+
+tasks {
+        jar {
+                dependsOn(webapp)
+                from(webapp) {
+                        into("webapp")
+                }
+        }
+
+        shadowJar {
+                dependsOn(webapp)
+                from(project.sourceSets.main.map { it.output })
+                exclude("META-INF/INDEX.LIST", "META-INF/*.SF", "META-INF/*.DSA", "META-INF/*.RSA", "schema/*",
+                                ".options", ".api_description", "*.profile", "about.*", "about_*.html", "about_files/*",
+                                "plugin.xml", "systembundle.properties", "profile.list", "META-INF/resources/xtext/**")
+                append("plugin.properties")
+                from(webapp) {
+                        into("webapp")
+                }
+        }
+
+        register<JavaExec>("serveBackend") {
+                dependsOn(webapp)
+                val mainRuntimeClasspath = sourceSets.main.map { it.runtimeClasspath }
+                dependsOn(mainRuntimeClasspath)
+                classpath(mainRuntimeClasspath)
+                mainClass.set(application.mainClass)
+                standardInput = System.`in`
+                val baseResource = webapp.incoming.artifacts.artifactFiles.first()
+                environment("BASE_RESOURCE", baseResource)
+                group = "run"
+                description = "Start a Jetty web server serving the Xtex API and assets."
+        }
+}
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/CacheControlFilter.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/CacheControlFilter.java
index fd2af1b2..53f78c3c 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/CacheControlFilter.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/CacheControlFilter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web;
 
 import jakarta.servlet.*;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebModule.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebModule.java
index 706413a9..b0197c01 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebModule.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebModule.java
@@ -1,15 +1,19 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.web;
 
-import org.eclipse.xtext.ide.ExecutorServiceProvider;
 import org.eclipse.xtext.web.server.XtextServiceDispatcher;
 import org.eclipse.xtext.web.server.model.IWebDocumentProvider;
 import org.eclipse.xtext.web.server.model.XtextWebDocumentAccess;
 import org.eclipse.xtext.web.server.occurrences.OccurrencesService;
 import tools.refinery.language.web.occurrences.ProblemOccurrencesService;
-import tools.refinery.language.web.xtext.VirtualThreadExecutorServiceProvider;
 import tools.refinery.language.web.xtext.server.push.PushServiceDispatcher;
 import tools.refinery.language.web.xtext.server.push.PushWebDocumentAccess;
 import tools.refinery.language.web.xtext.server.push.PushWebDocumentProvider;
@@ -33,8 +37,4 @@ public class ProblemWebModule extends AbstractProblemWebModule {
         public Class<? extends OccurrencesService> bindOccurrencesService() {
                 return ProblemOccurrencesService.class;
         }
-
-        public Class<? extends ExecutorServiceProvider> bindExecutorServiceProvider() {
-                return VirtualThreadExecutorServiceProvider.class;
-        }
 }
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSetup.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSetup.java
index 4738bc80..53a394d8 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSetup.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSetup.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.web;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSocketServlet.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSocketServlet.java
index df67b521..7b48cde8 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSocketServlet.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/ProblemWebSocketServlet.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web;
 
 import org.eclipse.xtext.util.DisposableRegistry;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/SecurityHeadersFilter.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/SecurityHeadersFilter.java
index c41db799..7b094fde 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/SecurityHeadersFilter.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/SecurityHeadersFilter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web;
 
 import jakarta.servlet.*;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/ServerLauncher.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/ServerLauncher.java
index f49f46ee..ad19e77d 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/ServerLauncher.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/ServerLauncher.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.web;
@@ -13,6 +19,7 @@ import org.eclipse.jetty.ee10.websocket.server.config.JettyWebSocketServletConta
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.util.resource.Resource;
 import org.eclipse.jetty.util.resource.ResourceFactory;
+import org.eclipse.jetty.util.thread.QueuedThreadPool;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import tools.refinery.language.web.config.BackendConfigServlet;
@@ -43,7 +50,8 @@ public class ServerLauncher {
         private final Server server;
 
         public ServerLauncher(InetSocketAddress bindAddress, String[] allowedOrigins, String webSocketUrl) {
-                server = VirtualThreadUtils.newServerWithVirtualThreadsThreadPool("jetty", bindAddress);
+                server = new Server(bindAddress);
+                ((QueuedThreadPool) server.getThreadPool()).setName("jetty");
                 var handler = new ServletContextHandler();
                 addSessionHandler(handler);
                 addProblemServlet(handler, allowedOrigins);
@@ -105,7 +113,7 @@ public class ServerLauncher {
                 var indexUrlInJar = ServerLauncher.class.getResource("/webapp/index.html");
                 if (indexUrlInJar != null) {
                         // If the app is packaged in the jar, serve it.
-                        URI webRootUri = null;
+                        URI webRootUri;
                         try {
                                 webRootUri = URI.create(indexUrlInJar.toURI().toASCIIString().replaceFirst("/index.html$", "/"));
                         } catch (URISyntaxException e) {
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/VirtualThreadUtils.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/VirtualThreadUtils.java
deleted file mode 100644
index a055e755..00000000
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/VirtualThreadUtils.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package tools.refinery.language.web;
-
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.server.ServerConnector;
-import org.eclipse.jetty.util.thread.QueuedThreadPool;
-import org.eclipse.jetty.util.thread.ThreadPool;
-
-import java.net.InetSocketAddress;
-import java.time.Duration;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-public final class VirtualThreadUtils {
-        private VirtualThreadUtils() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static ExecutorService newNamedVirtualThreadsExecutor(String name) {
-                // Based on
-                // https://github.com/eclipse/jetty.project/blob/83154b4ffe4767ef44981598d6c26e6a5d32e57c/jetty-server/src/main/config/etc/jetty-threadpool-virtual-preview.xml
-                return Executors.newThreadPerTaskExecutor(Thread.ofVirtual()
-                                .allowSetThreadLocals(true)
-                                .inheritInheritableThreadLocals(false)
-                                .name(name + "-virtual-", 0)
-                                .factory());
-        }
-
-        public static ThreadPool newThreadPoolWithVirtualThreadsExecutor(String name) {
-                // Based on
-                // https://github.com/eclipse/jetty.project/blob/83154b4ffe4767ef44981598d6c26e6a5d32e57c/jetty-server/src/main/config/etc/jetty-threadpool-virtual-preview.xml
-                int timeout = (int) Duration.ofMinutes(1).toMillis();
-                var threadPool = new QueuedThreadPool(200, 10, timeout, -1, null, null);
-                threadPool.setName(name);
-                threadPool.setDetailedDump(false);
-                threadPool.setVirtualThreadsExecutor(newNamedVirtualThreadsExecutor(name));
-                return threadPool;
-        }
-
-        public static Server newServerWithVirtualThreadsThreadPool(String name, InetSocketAddress listenAddress) {
-                var server = new Server(newThreadPoolWithVirtualThreadsExecutor(name));
-                var connector = new ServerConnector(server);
-                try {
-                        connector.setHost(listenAddress.getHostName());
-                        connector.setPort(listenAddress.getPort());
-                        server.addConnector(connector);
-                } catch (Exception e) {
-                        connector.close();
-                        throw e;
-                }
-                return server;
-        }
-}
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfig.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfig.java
index 2e864998..807b789c 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfig.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfig.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.config;
 
 import com.google.gson.annotations.SerializedName;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfigServlet.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfigServlet.java
index f314a9fa..a2f04e34 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfigServlet.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/config/BackendConfigServlet.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.config;
 
 import com.google.gson.Gson;
@@ -29,7 +34,7 @@ public class BackendConfigServlet extends HttpServlet {
         }
 
         @Override
-        protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
+        protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws IOException {
                 resp.setStatus(HttpStatus.OK_200);
                 resp.setContentType("application/json");
                 var writer = resp.getWriter();
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/occurrences/ProblemOccurrencesService.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/occurrences/ProblemOccurrencesService.java
index d32bbb54..34117384 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/occurrences/ProblemOccurrencesService.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/occurrences/ProblemOccurrencesService.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.occurrences;
 
 import org.eclipse.emf.ecore.EObject;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/VirtualThreadExecutorServiceProvider.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/VirtualThreadExecutorServiceProvider.java
deleted file mode 100644
index abbcbd53..00000000
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/VirtualThreadExecutorServiceProvider.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package tools.refinery.language.web.xtext;
-
-import org.eclipse.xtext.ide.ExecutorServiceProvider;
-import tools.refinery.language.web.VirtualThreadUtils;
-
-import java.util.concurrent.ExecutorService;
-
-public class VirtualThreadExecutorServiceProvider extends ExecutorServiceProvider {
-        private static final String THREAD_POOL_NAME = "xtextWeb";
-
-        @Override
-        protected ExecutorService createInstance(String key) {
-                var name = key == null ? THREAD_POOL_NAME : THREAD_POOL_NAME + "-" + key;
-                return VirtualThreadUtils.newNamedVirtualThreadsExecutor(name);
-        }
-}
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/PongResult.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/PongResult.java
index fe510f51..27b2e04e 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/PongResult.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/PongResult.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server;
 
 import java.util.Objects;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandler.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandler.java
index 2a85afe3..3069c2dd 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandler.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandler.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server;
 
 import tools.refinery.language.web.xtext.server.message.XtextWebResponse;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandlerException.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandlerException.java
index b686d33a..366ef0a7 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandlerException.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/ResponseHandlerException.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server;
 
 import java.io.Serial;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/SubscribingServiceContext.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/SubscribingServiceContext.java
index 78e00a9e..04212b84 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/SubscribingServiceContext.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/SubscribingServiceContext.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server;
 
 import java.util.Set;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/TransactionExecutor.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/TransactionExecutor.java
index 7bb11d2e..0135d8f5 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/TransactionExecutor.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/TransactionExecutor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server;
 
 import com.google.common.base.Strings;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorKind.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorKind.java
index f74bae74..6f4f265c 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorKind.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorKind.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 import com.google.gson.annotations.SerializedName;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorResponse.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorResponse.java
index 01d78c31..af38ad70 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorResponse.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebErrorResponse.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 import java.util.Objects;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebOkResponse.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebOkResponse.java
index 8af27247..73527ee5 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebOkResponse.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebOkResponse.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 import java.util.Objects;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebPushMessage.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebPushMessage.java
index c9432e1c..e9ff87c4 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebPushMessage.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebPushMessage.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 import java.util.Objects;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebRequest.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebRequest.java
index 959749f8..ff788e94 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebRequest.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebRequest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 import java.util.Map;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebResponse.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebResponse.java
index 3bd13047..61444c99 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebResponse.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/message/XtextWebResponse.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.message;
 
 public sealed interface XtextWebResponse permits XtextWebOkResponse,XtextWebErrorResponse,XtextWebPushMessage {
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PrecomputationListener.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PrecomputationListener.java
index 79a284db..110c8f52 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PrecomputationListener.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PrecomputationListener.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.push;
 
 import org.eclipse.xtext.web.server.IServiceResult;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushServiceDispatcher.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushServiceDispatcher.java
index c7b8108d..4c9135c8 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushServiceDispatcher.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushServiceDispatcher.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.push;
 
 import org.eclipse.xtext.web.server.IServiceContext;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocument.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocument.java
index 906b9e30..56fd12c9 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocument.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocument.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.push;
 
 import java.util.ArrayList;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentAccess.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentAccess.java
index b3666a86..d9e548cd 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentAccess.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentAccess.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.push;
 
 import org.eclipse.xtext.service.OperationCanceledManager;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentProvider.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentProvider.java
index b6f04748..b6f4fb43 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentProvider.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/server/push/PushWebDocumentProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.server.push;
 
 import org.eclipse.xtext.web.server.IServiceContext;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleServiceContext.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleServiceContext.java
index 43e37160..fee1141d 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleServiceContext.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleServiceContext.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 import java.util.Map;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleSession.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleSession.java
index 09c055a2..bc60c282 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleSession.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/SimpleSession.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 import java.util.HashMap;
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextStatusCode.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextStatusCode.java
index 0cd229e8..caa98e84 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextStatusCode.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextStatusCode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 public final class XtextStatusCode {
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
index 1d9e0463..043d318c 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocket.java
@@ -1,12 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 import com.google.gson.Gson;
 import com.google.gson.JsonIOException;
 import com.google.gson.JsonParseException;
-import org.eclipse.jetty.ee10.websocket.api.Session;
-import org.eclipse.jetty.ee10.websocket.api.StatusCode;
-import org.eclipse.jetty.ee10.websocket.api.WriteCallback;
-import org.eclipse.jetty.ee10.websocket.api.annotations.*;
+import org.eclipse.jetty.websocket.api.Callback;
+import org.eclipse.jetty.websocket.api.Session;
+import org.eclipse.jetty.websocket.api.StatusCode;
+import org.eclipse.jetty.websocket.api.annotations.*;
 import org.eclipse.xtext.resource.IResourceServiceProvider;
 import org.eclipse.xtext.web.server.ISession;
 import org.slf4j.Logger;
@@ -20,7 +25,7 @@ import tools.refinery.language.web.xtext.server.message.XtextWebResponse;
 import java.io.Reader;
 
 @WebSocket
-public class XtextWebSocket implements WriteCallback, ResponseHandler {
+public class XtextWebSocket implements ResponseHandler {
         private static final Logger LOG = LoggerFactory.getLogger(XtextWebSocket.class);
 
         private final Gson gson = new Gson();
@@ -38,13 +43,13 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                 this(new TransactionExecutor(session, resourceServiceProviderRegistry));
         }
 
-        @OnWebSocketConnect
-        public void onConnect(Session webSocketSession) {
+        @OnWebSocketOpen
+        public void onOpen(Session webSocketSession) {
                 if (this.webSocketSession != null) {
                         LOG.error("Websocket session onConnect when already connected");
                         return;
                 }
-                LOG.debug("New websocket connection from {}", webSocketSession.getRemoteAddress());
+                LOG.debug("New websocket connection from {}", webSocketSession.getRemoteSocketAddress());
                 this.webSocketSession = webSocketSession;
         }
 
@@ -55,10 +60,10 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                         return;
                 }
                 if (statusCode == StatusCode.NORMAL || statusCode == StatusCode.SHUTDOWN) {
-                        LOG.debug("{} closed connection normally: {}", webSocketSession.getRemoteAddress(), reason);
+                        LOG.debug("{} closed connection normally: {}", webSocketSession.getRemoteSocketAddress(), reason);
                 } else {
-                        LOG.warn("{} closed connection with status code {}: {}", webSocketSession.getRemoteAddress(), statusCode,
-                                        reason);
+                        LOG.warn("{} closed connection with status code {}: {}", webSocketSession.getRemoteSocketAddress(),
+                                        statusCode, reason);
                 }
                 webSocketSession = null;
         }
@@ -68,7 +73,7 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                 if (webSocketSession == null) {
                         return;
                 }
-                LOG.error("Internal websocket error in connection from" + webSocketSession.getRemoteAddress(), error);
+                LOG.error("Internal websocket error in connection from" + webSocketSession.getRemoteSocketAddress(), error);
         }
 
         @OnWebSocketMessage
@@ -81,14 +86,14 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                 try {
                         request = gson.fromJson(reader, XtextWebRequest.class);
                 } catch (JsonIOException e) {
-                        LOG.error("Cannot read from websocket from" + webSocketSession.getRemoteAddress(), e);
+                        LOG.error("Cannot read from websocket from" + webSocketSession.getRemoteSocketAddress(), e);
                         if (webSocketSession.isOpen()) {
-                                webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot read payload");
+                                webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot read payload", Callback.NOOP);
                         }
                         return;
                 } catch (JsonParseException e) {
-                        LOG.warn("Malformed websocket request from" + webSocketSession.getRemoteAddress(), e);
-                        webSocketSession.close(XtextStatusCode.INVALID_JSON, "Invalid JSON payload");
+                        LOG.warn("Malformed websocket request from" + webSocketSession.getRemoteSocketAddress(), e);
+                        webSocketSession.close(XtextStatusCode.INVALID_JSON, "Invalid JSON payload", Callback.NOOP);
                         return;
                 }
                 try {
@@ -96,7 +101,7 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                 } catch (ResponseHandlerException e) {
                         LOG.warn("Cannot write websocket response", e);
                         if (webSocketSession.isOpen()) {
-                                webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot write response");
+                                webSocketSession.close(StatusCode.SERVER_ERROR, "Cannot write response", Callback.NOOP);
                         }
                 }
         }
@@ -107,15 +112,14 @@ public class XtextWebSocket implements WriteCallback, ResponseHandler {
                         throw new ResponseHandlerException("Trying to send message when websocket is disconnected");
                 }
                 var responseString = gson.toJson(response);
-                webSocketSession.getRemote().sendPartialString(responseString, true, this);
+                webSocketSession.sendText(responseString, Callback.from(() -> {}, this::writeFailed));
         }
 
-        @Override
         public void writeFailed(Throwable x) {
                 if (webSocketSession == null) {
                         LOG.error("Cannot complete async write to disconnected websocket", x);
                         return;
                 }
-                LOG.warn("Cannot complete async write to websocket " + webSocketSession.getRemoteAddress(), x);
+                LOG.warn("Cannot complete async write to websocket " + webSocketSession.getRemoteSocketAddress(), x);
         }
 }
diff --git a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocketServlet.java b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocketServlet.java
index 9a32b937..5e4fb0ce 100644
--- a/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocketServlet.java
+++ b/subprojects/language-web/src/main/java/tools/refinery/language/web/xtext/servlet/XtextWebSocketServlet.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 import jakarta.servlet.ServletConfig;
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/ProblemWebSocketServletIntegrationTest.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/ProblemWebSocketServletIntegrationTest.java
index ecbefc4f..927eeab1 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/ProblemWebSocketServletIntegrationTest.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/ProblemWebSocketServletIntegrationTest.java
@@ -1,20 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web;
 
 import org.eclipse.jetty.ee10.servlet.ServletContextHandler;
 import org.eclipse.jetty.ee10.servlet.ServletHolder;
-import org.eclipse.jetty.ee10.websocket.api.Session;
-import org.eclipse.jetty.ee10.websocket.api.StatusCode;
-import org.eclipse.jetty.ee10.websocket.api.annotations.WebSocket;
-import org.eclipse.jetty.ee10.websocket.api.exceptions.UpgradeException;
-import org.eclipse.jetty.ee10.websocket.client.ClientUpgradeRequest;
-import org.eclipse.jetty.ee10.websocket.client.WebSocketClient;
 import org.eclipse.jetty.ee10.websocket.server.config.JettyWebSocketServletContainerInitializer;
 import org.eclipse.jetty.http.HttpHeader;
 import org.eclipse.jetty.http.HttpStatus;
 import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.util.thread.QueuedThreadPool;
+import org.eclipse.jetty.websocket.api.Callback;
+import org.eclipse.jetty.websocket.api.Session;
+import org.eclipse.jetty.websocket.api.StatusCode;
+import org.eclipse.jetty.websocket.api.annotations.WebSocket;
+import org.eclipse.jetty.websocket.api.exceptions.UpgradeException;
+import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
+import org.eclipse.jetty.websocket.client.WebSocketClient;
 import org.eclipse.xtext.testing.GlobalRegistries;
 import org.eclipse.xtext.testing.GlobalRegistries.GlobalStateMemento;
-import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInfo;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 import tools.refinery.language.web.tests.WebSocketIntegrationTestClient;
@@ -86,23 +96,34 @@ class ProblemWebSocketServletIntegrationTest {
                 assertThat(responses, hasSize(5));
                 assertThat(responses.get(0), equalTo("{\"id\":\"foo\",\"response\":{\"stateId\":\"-80000000\"}}"));
                 assertThat(responses.get(1), startsWith(
-                                "{\"resource\":\"test.problem\",\"stateId\":\"-80000000\",\"service\":\"highlight\",\"push\":{\"regions\":["));
+                                "{\"resource\":\"test.problem\",\"stateId\":\"-80000000\",\"service\":\"highlight\"," +
+                                                "\"push\":{\"regions\":["));
                 assertThat(responses.get(2), equalTo(
-                                "{\"resource\":\"test.problem\",\"stateId\":\"-80000000\",\"service\":\"validate\",\"push\":{\"issues\":[]}}"));
+                                "{\"resource\":\"test.problem\",\"stateId\":\"-80000000\",\"service\":\"validate\"," +
+                                                "\"push\":{\"issues\":[]}}"));
                 assertThat(responses.get(3), equalTo("{\"id\":\"bar\",\"response\":{\"stateId\":\"-7fffffff\"}}"));
                 assertThat(responses.get(4), startsWith(
-                                "{\"resource\":\"test.problem\",\"stateId\":\"-7fffffff\",\"service\":\"highlight\",\"push\":{\"regions\":["));
+                                "{\"resource\":\"test.problem\",\"stateId\":\"-7fffffff\",\"service\":\"highlight\"," +
+                                                "\"push\":{\"regions\":["));
         }
 
         @WebSocket
         public static class UpdateTestClient extends WebSocketIntegrationTestClient {
                 @Override
-                protected void arrange(Session session, int responsesReceived) throws IOException {
+                protected void arrange(Session session, int responsesReceived) {
                         switch (responsesReceived) {
-                        case 0 -> session.getRemote().sendString(
-                                        "{\"id\":\"foo\",\"request\":{\"resource\":\"test.problem\",\"serviceType\":\"update\",\"fullText\":\"class Person.\n\"}}");
-                        case 3 -> session.getRemote().sendString(
-                                        "{\"id\":\"bar\",\"request\":{\"resource\":\"test.problem\",\"serviceType\":\"update\",\"requiredStateId\":\"-80000000\",\"deltaText\":\"indiv q.\nnode(q).\n\",\"deltaOffset\":\"0\",\"deltaReplaceLength\":\"0\"}}");
+                        case 0 -> session.sendText(
+                                        "{\"id\":\"foo\",\"request\":{\"resource\":\"test.problem\",\"serviceType\":\"update\"," +
+                                                        "\"fullText\":\"class Person.\n\"}}",
+                                        Callback.NOOP
+                        );
+                        case 3 -> //noinspection TextBlockMigration
+                                        session.sendText(
+                                        "{\"id\":\"bar\",\"request\":{\"resource\":\"test.problem\",\"serviceType\":\"update\"," +
+                                                        "\"requiredStateId\":\"-80000000\",\"deltaText\":\"indiv q.\nnode(q).\n\"," +
+                                                        "\"deltaOffset\":\"0\",\"deltaReplaceLength\":\"0\"}}",
+                                        Callback.NOOP
+                        );
                         case 5 -> session.close();
                         }
                 }
@@ -152,13 +173,13 @@ class ProblemWebSocketServletIntegrationTest {
         @WebSocket
         public static class InvalidJsonTestClient extends WebSocketIntegrationTestClient {
                 @Override
-                protected void arrange(Session session, int responsesReceived) throws IOException {
-                        session.getRemote().sendString("<invalid json>");
+                protected void arrange(Session session, int responsesReceived) {
+                        session.sendText("<invalid json>", Callback.NOOP);
                 }
         }
 
         @ParameterizedTest(name = "validOriginTest(\"{0}\")")
-        @ValueSource(strings = { "https://refinery.example", "https://refinery.example:443", "HTTPS://REFINERY.EXAMPLE" })
+        @ValueSource(strings = {"https://refinery.example", "https://refinery.example:443", "HTTPS://REFINERY.EXAMPLE"})
         void validOriginTest(String origin) {
                 startServer("https://refinery.example,https://refinery.example:443");
                 var clientSocket = new CloseImmediatelyTestClient();
@@ -188,7 +209,8 @@ class ProblemWebSocketServletIntegrationTest {
         private void startServer(String allowedOrigins) {
                 var testName = getClass().getSimpleName() + "-" + testInfo.getDisplayName();
                 var listenAddress = new InetSocketAddress(HOSTNAME, serverPort);
-                server = VirtualThreadUtils.newServerWithVirtualThreadsThreadPool(testName, listenAddress);
+                server = new Server(listenAddress);
+                ((QueuedThreadPool) server.getThreadPool()).setName(testName);
                 var handler = new ServletContextHandler();
                 var holder = new ServletHolder(ProblemWebSocketServlet.class);
                 if (allowedOrigins != null) {
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/AwaitTerminationExecutorServiceProvider.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/AwaitTerminationExecutorServiceProvider.java
index c634e8fc..52acee6d 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/AwaitTerminationExecutorServiceProvider.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/AwaitTerminationExecutorServiceProvider.java
@@ -1,14 +1,19 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.tests;
 
 import com.google.inject.Singleton;
-import tools.refinery.language.web.xtext.VirtualThreadExecutorServiceProvider;
+import org.eclipse.xtext.ide.ExecutorServiceProvider;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
 
 @Singleton
-public class AwaitTerminationExecutorServiceProvider extends VirtualThreadExecutorServiceProvider {
+public class AwaitTerminationExecutorServiceProvider extends ExecutorServiceProvider {
         private final List<RestartableCachedThreadPool> servicesToShutDown = new ArrayList<>();
 
         @Override
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/ProblemWebInjectorProvider.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/ProblemWebInjectorProvider.java
index 43c12faa..4a5eed95 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/ProblemWebInjectorProvider.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/ProblemWebInjectorProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.tests;
 
 import org.eclipse.xtext.ide.ExecutorServiceProvider;
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/RestartableCachedThreadPool.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/RestartableCachedThreadPool.java
index cf805eda..09079aa8 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/RestartableCachedThreadPool.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/RestartableCachedThreadPool.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.tests;
 
 import com.google.inject.Provider;
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/WebSocketIntegrationTestClient.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/WebSocketIntegrationTestClient.java
index f19c10ca..6ccf1760 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/WebSocketIntegrationTestClient.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/tests/WebSocketIntegrationTestClient.java
@@ -1,12 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.tests;
 
-import org.eclipse.jetty.ee10.websocket.api.Session;
-import org.eclipse.jetty.ee10.websocket.api.annotations.OnWebSocketClose;
-import org.eclipse.jetty.ee10.websocket.api.annotations.OnWebSocketConnect;
-import org.eclipse.jetty.ee10.websocket.api.annotations.OnWebSocketError;
-import org.eclipse.jetty.ee10.websocket.api.annotations.OnWebSocketMessage;
+import org.eclipse.jetty.websocket.api.Session;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketClose;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketError;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketOpen;
 
-import java.io.IOException;
 import java.time.Duration;
 import java.util.ArrayList;
 import java.util.List;
@@ -14,7 +18,7 @@ import java.util.List;
 import static org.junit.jupiter.api.Assertions.fail;
 
 public abstract class WebSocketIntegrationTestClient {
-        private static final long TIMEOUT_MILLIS = Duration.ofSeconds(1).toMillis();
+        private static final long TIMEOUT_MILLIS = Duration.ofSeconds(10).toMillis();
 
         private boolean finished = false;
 
@@ -34,8 +38,8 @@ public abstract class WebSocketIntegrationTestClient {
                 return responses;
         }
 
-        @OnWebSocketConnect
-        public void onConnect(Session session) {
+        @OnWebSocketOpen
+        public void onOpen(Session session) {
                 arrangeAndCatchErrors(session);
         }
 
@@ -47,7 +51,7 @@ public abstract class WebSocketIntegrationTestClient {
                 }
         }
 
-        protected abstract void arrange(Session session, int responsesReceived) throws IOException;
+        protected abstract void arrange(Session session, int responsesReceived);
 
         @OnWebSocketClose
         public void onClose(int statusCode, String reason) {
diff --git a/subprojects/language-web/src/test/java/tools/refinery/language/web/xtext/servlet/TransactionExecutorTest.java b/subprojects/language-web/src/test/java/tools/refinery/language/web/xtext/servlet/TransactionExecutorTest.java
index 17f1ff5c..841bacd3 100644
--- a/subprojects/language-web/src/test/java/tools/refinery/language/web/xtext/servlet/TransactionExecutorTest.java
+++ b/subprojects/language-web/src/test/java/tools/refinery/language/web/xtext/servlet/TransactionExecutorTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.web.xtext.servlet;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/build.gradle b/subprojects/language/build.gradle
deleted file mode 100644
index 654558e3..00000000
--- a/subprojects/language/build.gradle
+++ /dev/null
@@ -1,73 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-        id 'refinery-java-test-fixtures'
-        id 'refinery-mwe2'
-        id 'refinery-sonarqube'
-        id 'refinery-xtext-conventions'
-}
-
-dependencies {
-        api platform(libs.xtext.bom)
-        api libs.ecore
-        api libs.xtext.core
-        api libs.xtext.xbase
-        api project(':refinery-language-model')
-        testFixturesApi libs.xtext.testing
-        mwe2 libs.xtext.generator
-        mwe2 libs.xtext.generator.antlr
-}
-
-sourceSets {
-        testFixtures {
-                java.srcDirs += ['src/testFixtures/xtext-gen']
-                resources.srcDirs += ['src/testFixtures/xtext-gen']
-        }
-}
-
-tasks.named('jar') {
-        from(sourceSets.main.allSource) {
-                include '**/*.xtext'
-        }
-}
-
-def generateXtextLanguage = tasks.register('generateXtextLanguage', JavaExec) {
-        mainClass = 'org.eclipse.emf.mwe2.launch.runtime.Mwe2Launcher'
-        classpath = configurations.mwe2
-        inputs.file 'src/main/java/tools/refinery/language/GenerateProblem.mwe2'
-        inputs.file 'src/main/java/tools/refinery/language/Problem.xtext'
-        outputs.dir 'src/main/xtext-gen'
-        outputs.dir 'src/testFixtures/xtext-gen'
-        outputs.dir '../language-ide/src/main/xtext-gen'
-        outputs.dir '../language-web/src/main/xtext-gen'
-        args += 'src/main/java/tools/refinery/language/GenerateProblem.mwe2'
-        args += '-p'
-        args += "rootPath=/${projectDir}/.."
-}
-
-for (taskName in [
-                'compileJava',
-                'processResources',
-                'processTestFixturesResources',
-                'generateEclipseSourceFolders'
-        ]) {
-        tasks.named(taskName) {
-                dependsOn generateXtextLanguage
-        }
-}
-
-tasks.named('clean') {
-        delete 'src/main/xtext-gen'
-        delete 'src/testFixtures/xtext-gen'
-        delete '../language-ide/src/main/xtext-gen'
-        delete '../language-web/src/main/xtext-gen'
-}
-
-sonarqube.properties {
-        properties['sonar.exclusions'] += [
-                'src/testFixtures/xtext-gen/**',
-        ]
-}
-
-eclipse.project.natures += [
-        'org.eclipse.xtext.ui.shared.xtextNature'
-]
diff --git a/subprojects/language/build.gradle.kts b/subprojects/language/build.gradle.kts
new file mode 100644
index 00000000..bac1e586
--- /dev/null
+++ b/subprojects/language/build.gradle.kts
@@ -0,0 +1,101 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+import tools.refinery.gradle.utils.SonarPropertiesUtils
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+        id("tools.refinery.gradle.java-test-fixtures")
+        id("tools.refinery.gradle.mwe2")
+        id("tools.refinery.gradle.sonarqube")
+        id("tools.refinery.gradle.xtext-generated")
+}
+
+val generatedIdeSources: Configuration by configurations.creating {
+        isCanBeConsumed = true
+        isCanBeResolved = false
+}
+
+val generatedWebSources: Configuration by configurations.creating {
+        isCanBeConsumed = true
+        isCanBeResolved = false
+}
+
+dependencies {
+        api(platform(libs.xtext.bom))
+        api(libs.ecore)
+        api(libs.xtext.core)
+        api(libs.xtext.xbase)
+        api(project(":refinery-language-model"))
+        testFixturesApi(libs.xtext.testing)
+        mwe2(libs.xtext.generator)
+        mwe2(libs.xtext.generator.antlr)
+}
+
+sourceSets {
+        testFixtures {
+                java.srcDir("src/testFixtures/xtext-gen")
+                resources.srcDir("src/testFixtures/xtext-gen")
+        }
+}
+
+val generateXtextLanguage by tasks.registering(JavaExec::class) {
+        mainClass.set("org.eclipse.emf.mwe2.launch.runtime.Mwe2Launcher")
+        classpath(configurations.mwe2)
+        inputs.file("src/main/java/tools/refinery/language/GenerateProblem.mwe2")
+        inputs.file("src/main/java/tools/refinery/language/Problem.xtext")
+        inputs.file("../language-model/src/main/resources/model/problem.ecore")
+        inputs.file("../language-model/src/main/resources/model/problem.genmodel")
+        outputs.dir("src/main/xtext-gen")
+        outputs.dir("src/testFixtures/xtext-gen")
+        outputs.dir("$buildDir/generated/sources/xtext/ide")
+        outputs.dir("$buildDir/generated/sources/xtext/web")
+        args("src/main/java/tools/refinery/language/GenerateProblem.mwe2", "-p", "rootPath=/$projectDir/..")
+}
+
+tasks {
+        jar {
+                from(sourceSets.main.map { it.allSource }) {
+                        include("**/*.xtext")
+                }
+        }
+
+        syncXtextGeneratedSources {
+                // We generate Xtext runtime sources directly to {@code src/main/xtext-gen}, so there is no need to copy them
+                // from an artifact. We expose the {@code generatedIdeSources} and {@code generatedWebSources} artifacts to
+                // sibling IDE and web projects which can use this task to consume them and copy the appropriate sources to
+                // their own {@code src/main/xtext-gen} directory.
+                enabled = false
+        }
+
+        for (taskName in listOf("compileJava", "processResources", "compileTestFixturesJava",
+                        "processTestFixturesResources", "generateEclipseSourceFolders")) {
+                named(taskName) {
+                        dependsOn(generateXtextLanguage)
+                }
+        }
+
+        clean {
+                delete("src/main/xtext-gen")
+                delete("src/testFixtures/xtext-gen")
+        }
+}
+
+artifacts {
+        add(generatedIdeSources.name, file("$buildDir/generated/sources/xtext/ide")) {
+                builtBy(generateXtextLanguage)
+        }
+
+        add(generatedWebSources.name, file("$buildDir/generated/sources/xtext/web")) {
+                builtBy(generateXtextLanguage)
+        }
+}
+
+sonarqube.properties {
+        SonarPropertiesUtils.addToList(properties, "sonar.exclusions", "src/textFixtures/xtext-gen/**")
+}
+
+eclipse.project.natures.plusAssign("org.eclipse.xtext.ui.shared.xtextNature")
diff --git a/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2 b/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
index 21ff456e..59eba8f7 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
+++ b/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 module tools.refinery.language.GenerateProblem
 
 import org.eclipse.xtext.xtext.generator.*
@@ -11,16 +16,28 @@ Workflow {
                         project = StandardProjectConfig {
                                 baseName = 'language'
                                 rootPath = rootPath
+                                runtime = {
+                                        // Do not generate new files into src/main/java
+                                        src = null
+                                }
                                 runtimeTest = {
                                         enabled = true
-                                        srcGen = 'src/testFixtures/xtext-gen'
+                                        // Only generate the xtext-gen files and leave the rest of the project alone
+                                        root = null
+                                        srcGen = '${rootPath}/language/src/testFixtures/xtext-gen'
                                 }
                                 genericIde = {
                                         name = 'language-ide'
+                                        // Only generate the xtext-gen files and leave the rest of the project alone
+                                        root = null
+                                        srcGen = "${rootPath}/language/build/generated/sources/xtext/ide"
                                 }
                                 web = {
                                         enabled = true
                                         name = 'language-web'
+                                        // Only generate the xtext-gen files and leave the rest of the project alone
+                                        root = null
+                                        srcGen = "${rootPath}/language/build/generated/sources/xtext/web"
                                 }
                                 mavenLayout = true
                         }
@@ -55,7 +72,7 @@ Workflow {
                         }
                         webSupport = {
                                 // We only generate the {@code AbstractProblemWebModule},
-                                // because we write our own integration code for CodeMirror 6. 
+                                // because we write our own integration code for CodeMirror 6.
                                 framework = 'codemirror'
                                 generateHtmlExample = false
                                 generateJettyLauncher = false
diff --git a/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext b/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
index 187ebf1f..9e330347 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
+++ b/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 grammar tools.refinery.language.Problem with org.eclipse.xtext.common.Terminals
 
 import "http://www.eclipse.org/emf/2002/Ecore" as ecore
diff --git a/subprojects/language/src/main/java/tools/refinery/language/ProblemRuntimeModule.java b/subprojects/language/src/main/java/tools/refinery/language/ProblemRuntimeModule.java
index 5efcdc81..2636a8ee 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/ProblemRuntimeModule.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/ProblemRuntimeModule.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/ProblemStandaloneSetup.java b/subprojects/language/src/main/java/tools/refinery/language/ProblemStandaloneSetup.java
index 41c96114..639d6778 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/ProblemStandaloneSetup.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/ProblemStandaloneSetup.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/conversion/ProblemValueConverterService.java b/subprojects/language/src/main/java/tools/refinery/language/conversion/ProblemValueConverterService.java
index 508688ed..afbc367e 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/conversion/ProblemValueConverterService.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/conversion/ProblemValueConverterService.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.conversion;
 
 import org.eclipse.xtext.common.services.DefaultTerminalConverters;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/conversion/UpperBoundValueConverter.java b/subprojects/language/src/main/java/tools/refinery/language/conversion/UpperBoundValueConverter.java
index be0d15ad..4886757d 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/conversion/UpperBoundValueConverter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/conversion/UpperBoundValueConverter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.conversion;
 
 import org.eclipse.xtext.conversion.ValueConverterException;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java b/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
index 797535ea..55a5ac20 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.26.0.M2
  */
 package tools.refinery.language.formatting2;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/naming/NamingUtil.java b/subprojects/language/src/main/java/tools/refinery/language/naming/NamingUtil.java
index e959be74..1647d4e7 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/naming/NamingUtil.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/naming/NamingUtil.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.naming;
 
 import java.util.regex.Pattern;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/naming/ProblemQualifiedNameConverter.java b/subprojects/language/src/main/java/tools/refinery/language/naming/ProblemQualifiedNameConverter.java
index 5453906f..74b4e208 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/naming/ProblemQualifiedNameConverter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/naming/ProblemQualifiedNameConverter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.naming;
 
 import org.eclipse.xtext.naming.IQualifiedNameConverter;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/IdentifierTokenProvider.java b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/IdentifierTokenProvider.java
index ab133a90..306a86fc 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/IdentifierTokenProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/IdentifierTokenProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.parser.antlr;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/ProblemTokenSource.java b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/ProblemTokenSource.java
index 0b4e7185..5b91a6cc 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/ProblemTokenSource.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/ProblemTokenSource.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.29.0.M2
  */
 package tools.refinery.language.parser.antlr;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/TokenSourceInjectingProblemParser.java b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/TokenSourceInjectingProblemParser.java
index 0cdd38d8..fe4c0bc7 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/TokenSourceInjectingProblemParser.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/parser/antlr/TokenSourceInjectingProblemParser.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.parser.antlr;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/DerivedVariableComputer.java b/subprojects/language/src/main/java/tools/refinery/language/resource/DerivedVariableComputer.java
index 6176b0c4..07c5da41 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/DerivedVariableComputer.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/DerivedVariableComputer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ImplicitVariableScope.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ImplicitVariableScope.java
index b0ac2ab6..e97c8287 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ImplicitVariableScope.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ImplicitVariableScope.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import org.eclipse.emf.ecore.EObject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/NodeNameCollector.java b/subprojects/language/src/main/java/tools/refinery/language/resource/NodeNameCollector.java
index 419be0d3..e5deca4d 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/NodeNameCollector.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/NodeNameCollector.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import com.google.common.collect.ImmutableSet;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemDerivedStateComputer.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemDerivedStateComputer.java
index 8d3a552a..b145ef27 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemDerivedStateComputer.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemDerivedStateComputer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
index df822987..1fe2df89 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import org.eclipse.emf.ecore.EObject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
index 1a0b73a8..630be379 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import org.eclipse.emf.ecore.EObject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ReferenceCounter.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ReferenceCounter.java
index ca20325e..f1be55ee 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ReferenceCounter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ReferenceCounter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.resource;
 
 import java.util.HashMap;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemGlobalScopeProvider.java b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemGlobalScopeProvider.java
index b749154c..4d2dd772 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemGlobalScopeProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemGlobalScopeProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.scoping;
 
 import java.util.LinkedHashSet;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemLocalScopeProvider.java b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemLocalScopeProvider.java
index 61883f0e..229960a0 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemLocalScopeProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemLocalScopeProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.scoping;
 
 import java.util.List;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemScopeProvider.java b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemScopeProvider.java
index 3ab07496..cf099aba 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemScopeProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/scoping/ProblemScopeProvider.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.scoping;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/serializer/PreferShortAssertionsProblemSemanticSequencer.java b/subprojects/language/src/main/java/tools/refinery/language/serializer/PreferShortAssertionsProblemSemanticSequencer.java
index 27ce1521..b9cafbc2 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/serializer/PreferShortAssertionsProblemSemanticSequencer.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/serializer/PreferShortAssertionsProblemSemanticSequencer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.serializer;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/BuiltinSymbols.java b/subprojects/language/src/main/java/tools/refinery/language/utils/BuiltinSymbols.java
index d3777cd3..c8c7fd4a 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/BuiltinSymbols.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/BuiltinSymbols.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import tools.refinery.language.model.problem.*;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/CollectedSymbols.java b/subprojects/language/src/main/java/tools/refinery/language/utils/CollectedSymbols.java
index b5682f32..e4e4d07a 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/CollectedSymbols.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/CollectedSymbols.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import java.util.Map;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/ContainmentRole.java b/subprojects/language/src/main/java/tools/refinery/language/utils/ContainmentRole.java
index 708e10a9..a43c7dfe 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/ContainmentRole.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/ContainmentRole.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import tools.refinery.language.model.problem.PredicateKind;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/NodeInfo.java b/subprojects/language/src/main/java/tools/refinery/language/utils/NodeInfo.java
index c8f47653..0fa7a454 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/NodeInfo.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/NodeInfo.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 public record NodeInfo(String name, boolean individual) {
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemDesugarer.java b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemDesugarer.java
index b8200919..738a0896 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemDesugarer.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemDesugarer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
index 1e5164d3..9486dc2a 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import org.eclipse.emf.common.util.URI;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/RelationInfo.java b/subprojects/language/src/main/java/tools/refinery/language/utils/RelationInfo.java
index 2253d257..1c46fe72 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/RelationInfo.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/RelationInfo.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import tools.refinery.language.model.problem.*;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/SymbolCollector.java b/subprojects/language/src/main/java/tools/refinery/language/utils/SymbolCollector.java
index 65167ed6..a4ea1113 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/SymbolCollector.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/SymbolCollector.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.utils;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java b/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
index 659d882c..88d50c5b 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
@@ -1,4 +1,10 @@
 /*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+/*
  * generated by Xtext 2.25.0
  */
 package tools.refinery.language.validation;
diff --git a/subprojects/language/src/main/resources/tools/refinery/language/builtin.problem b/subprojects/language/src/main/resources/tools/refinery/language/builtin.problem
index 06b6da1d..9c1d7669 100644
--- a/subprojects/language/src/main/resources/tools/refinery/language/builtin.problem
+++ b/subprojects/language/src/main/resources/tools/refinery/language/builtin.problem
@@ -1,3 +1,6 @@
+% SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+%
+% SPDX-License-Identifier: EPL-2.0
 problem builtin.
 
 abstract class node {
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
index 58daa365..c7952369 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
index 6e0802ca..f688d970 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.formatting2;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/IdentifierTokenProviderTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/IdentifierTokenProviderTest.java
index abff8d9c..37d38dd9 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/IdentifierTokenProviderTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/IdentifierTokenProviderTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.parser.antlr;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/ProblemTokenSourceTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/ProblemTokenSourceTest.java
index cb42d5d0..644744a0 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/ProblemTokenSourceTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/ProblemTokenSourceTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.parser.antlr;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/TransitiveClosureParserTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/TransitiveClosureParserTest.java
index 65ceb45f..1180d131 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/TransitiveClosureParserTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/parser/antlr/TransitiveClosureParserTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.parser.antlr;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/rules/RuleParsingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/rules/RuleParsingTest.java
index 72e5e18a..68514bfa 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/rules/RuleParsingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/rules/RuleParsingTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.rules;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
index fa462691..734bfcd1 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.scoping;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
index 4a18704a..3f3a081f 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.serializer;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/utils/SymbolCollectorTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/utils/SymbolCollectorTest.java
index af6de37f..d200eeff 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/utils/SymbolCollectorTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/utils/SymbolCollectorTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.tests.utils;
 
 import com.google.inject.Inject;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemNavigationUtil.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemNavigationUtil.java
index 5761935b..d92011a9 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemNavigationUtil.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemNavigationUtil.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import java.util.List;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemParseHelper.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemParseHelper.java
index 5e044a94..6f6a87f7 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemParseHelper.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/ProblemParseHelper.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import org.eclipse.xtext.testing.util.ParseHelper;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAction.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAction.java
index d176727b..3a49a0b9 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAction.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAction.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Action;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedArgument.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedArgument.java
index 9e4c59f5..ed749fed 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedArgument.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedArgument.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.*;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertion.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertion.java
index 2c38639d..b2ef6e48 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertion.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertion.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Assertion;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertionArgument.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertionArgument.java
index 840c1f74..b36f2506 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertionArgument.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAssertionArgument.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.AssertionArgument;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAtom.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAtom.java
index 498991f8..c02f447b 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAtom.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedAtom.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Atom;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedClassDeclaration.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedClassDeclaration.java
index 41b2ea62..a228137c 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedClassDeclaration.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedClassDeclaration.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.ClassDeclaration;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConjunction.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConjunction.java
index 88ff71ab..b126b1ce 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConjunction.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConjunction.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Conjunction;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConsequent.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConsequent.java
index 46faa7da..8d6a92f8 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConsequent.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedConsequent.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Consequent;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedEnumDeclaration.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedEnumDeclaration.java
index 74dcf01b..229a8c0a 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedEnumDeclaration.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedEnumDeclaration.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.EnumDeclaration;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedLiteral.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedLiteral.java
index 4aa71b99..160e5dd8 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedLiteral.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedLiteral.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Atom;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedParametricDefinition.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedParametricDefinition.java
index c2f18a60..d44b79ed 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedParametricDefinition.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedParametricDefinition.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.Parameter;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedPredicateDefinition.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedPredicateDefinition.java
index 7b95ecc1..2cf5fd89 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedPredicateDefinition.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedPredicateDefinition.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.PredicateDefinition;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
index 78ca95c7..e5aa0043 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import org.eclipse.emf.ecore.resource.Resource.Diagnostic;
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedRuleDefinition.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedRuleDefinition.java
index a4cf2eaf..326d8ec3 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedRuleDefinition.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedRuleDefinition.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.language.model.tests.utils;
 
 import tools.refinery.language.model.problem.RuleDefinition;
diff --git a/subprojects/store-query-viatra/NOTICE.md b/subprojects/store-query-viatra/NOTICE.md
new file mode 100644
index 00000000..7c21726a
--- /dev/null
+++ b/subprojects/store-query-viatra/NOTICE.md
@@ -0,0 +1,87 @@
+<!--
+  Copyright (c) 2018-2019, Zoltan Ujhelyi, IncQuery Labs Ltd.
+  Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+
+  SPDX-License-Identifier: EPL-2.0
+-->
+
+This module contains source code from the [Eclipse VIATRA project](https://projects.eclipse.org/projects/modeling.viatra), which is available under the terms of the [Eclipse Public License v 2.0](http://www.eclipse.org/legal/epl-v20.html).
+
+We reproduce the [accompanying notices](https://github.com/viatra/org.eclipse.viatra/blob/d422bcc626a99c4640c0d13931f393ccea0d2326/NOTICE.md) in full below:
+
+# Notices for Eclipse VIATRA
+
+This content is produced and maintained by the Eclipse VIATRA project.
+
+* Project home: https://projects.eclipse.org/projects/modeling.viatra
+
+## Trademarks
+
+Eclipse VIATRA, and VIATRA are trademarks of the Eclipse Foundation.
+
+## Copyright
+
+All content is the property of the respective authors or their employers. For
+more information regarding authorship of content, please consult the listed
+source code repository logs.
+
+## Declared Project Licenses
+
+This program and the accompanying materials are made available under the terms
+of the Eclipse Public License v. 2.0 which is available at
+http://www.eclipse.org/legal/epl-v20.html.
+
+SPDX-License-Identifier: EPL-2.0
+
+## Source Code
+
+The project maintains the following source code repositories:
+
+* http://git.eclipse.org/c/viatra/org.eclipse.viatra.git
+* http://git.eclipse.org/c/viatra/org.eclipse.viatra.modelobfuscator.git
+* http://git.eclipse.org/c/viatra/org.eclipse.viatra.examples.git
+* http://git.eclipse.org/c/viatra/org.eclipse.viatra2.vpm.git
+
+## Third-party Content
+
+This project leverages the following third party content.
+
+ANTLR Runtime only: (3.2)
+
+* License: New BSD license
+
+Apache Commons Language Library (2.1)
+
+* License: Apache License, 2.0
+
+Google Guice / Inject Core API (3.0.0)
+
+* License: Apache License, 2.0
+
+Google Guice / Inject Core API (3.0.0)
+
+* License: Apache License 2.0
+
+Guava (10.0.1)
+
+* License: Apache License, 2.0
+
+Guice (2.0)
+
+* License: Apache License, 2.0
+
+guice-multibindings (3.0.0)
+
+* License: Apache License, 2.0
+
+log4j (1.2.15)
+
+* License: Apache License 2.0
+
+LPG Java Runtime (lpgjavaruntime.jar) (1.1)
+
+* License: Eclipse Public License
+
+mockito (1.9.5)
+
+* License: Apache License, 2.0, New BSD license, MIT license
diff --git a/subprojects/store-query-viatra/build.gradle b/subprojects/store-query-viatra/build.gradle
deleted file mode 100644
index c12b48fe..00000000
--- a/subprojects/store-query-viatra/build.gradle
+++ /dev/null
@@ -1,16 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-}
-
-configurations.testRuntimeClasspath {
-        // VIATRA requires log4j 1.x, but we use log4j-over-slf4j instead
-        exclude group: 'log4j', module: 'log4j'
-}
-
-dependencies {
-        implementation libs.ecore
-        api libs.viatra
-        api project(':refinery-store')
-        testImplementation libs.slf4j.simple
-        testImplementation libs.slf4j.log4j
-}
diff --git a/subprojects/store-query-viatra/build.gradle.kts b/subprojects/store-query-viatra/build.gradle.kts
new file mode 100644
index 00000000..e3a22145
--- /dev/null
+++ b/subprojects/store-query-viatra/build.gradle.kts
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+}
+
+dependencies {
+        implementation(libs.ecore)
+        api(libs.viatra)
+        api(project(":refinery-store-query"))
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQuery.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQuery.java
deleted file mode 100644
index 677e3c7d..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQuery.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package tools.refinery.store.query.viatra;
-
-import tools.refinery.store.adapter.ModelAdapterBuilderFactory;
-import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.ModelQuery;
-import tools.refinery.store.query.viatra.internal.ViatraModelQueryBuilderImpl;
-
-public final class ViatraModelQuery extends ModelAdapterBuilderFactory<ViatraModelQueryAdapter,
-                ViatraModelQueryStoreAdapter, ViatraModelQueryBuilder> {
-        public static final ViatraModelQuery ADAPTER = new ViatraModelQuery();
-
-        private ViatraModelQuery() {
-                super(ViatraModelQueryAdapter.class, ViatraModelQueryStoreAdapter.class, ViatraModelQueryBuilder.class);
-                extendsAdapter(ModelQuery.ADAPTER);
-        }
-
-        @Override
-        public ViatraModelQueryBuilder createBuilder(ModelStoreBuilder storeBuilder) {
-                return new ViatraModelQueryBuilderImpl(storeBuilder);
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryAdapter.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryAdapter.java
index 7e21476b..12c93f62 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryAdapter.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryAdapter.java
@@ -1,8 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra;
 
 import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryBuilderImpl;
 
 public interface ViatraModelQueryAdapter extends ModelQueryAdapter {
         @Override
         ViatraModelQueryStoreAdapter getStoreAdapter();
+
+        static ViatraModelQueryBuilder builder() {
+                return new ViatraModelQueryBuilderImpl();
+        }
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryBuilder.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryBuilder.java
index efc6146c..931a07aa 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryBuilder.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryBuilder.java
@@ -1,10 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra;
 
 import org.eclipse.viatra.query.runtime.api.ViatraQueryEngineOptions;
 import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackendFactory;
 import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.DNF;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.dnf.Dnf;
 import tools.refinery.store.query.ModelQueryBuilder;
 
 import java.util.Collection;
@@ -23,26 +29,26 @@ public interface ViatraModelQueryBuilder extends ModelQueryBuilder {
         ViatraModelQueryBuilder searchBackend(IQueryBackendFactory queryBackendFactory);
 
         @Override
-        default ViatraModelQueryBuilder queries(DNF... queries) {
+        default ViatraModelQueryBuilder queries(AnyQuery... queries) {
                 ModelQueryBuilder.super.queries(queries);
                 return this;
         }
 
         @Override
-        default ViatraModelQueryBuilder queries(Collection<DNF> queries) {
+        default ViatraModelQueryBuilder queries(Collection<? extends AnyQuery> queries) {
                 ModelQueryBuilder.super.queries(queries);
                 return this;
         }
 
         @Override
-        ViatraModelQueryBuilder query(DNF query);
+        ViatraModelQueryBuilder query(AnyQuery query);
 
-        ViatraModelQueryBuilder query(DNF query, QueryEvaluationHint queryEvaluationHint);
+        ViatraModelQueryBuilder query(AnyQuery query, QueryEvaluationHint queryEvaluationHint);
 
-        ViatraModelQueryBuilder computeHint(Function<DNF, QueryEvaluationHint> computeHint);
+        ViatraModelQueryBuilder computeHint(Function<Dnf, QueryEvaluationHint> computeHint);
 
-        ViatraModelQueryBuilder hint(DNF dnf, QueryEvaluationHint queryEvaluationHint);
+        ViatraModelQueryBuilder hint(Dnf dnf, QueryEvaluationHint queryEvaluationHint);
 
         @Override
-        ViatraModelQueryStoreAdapter createStoreAdapter(ModelStore store);
+        ViatraModelQueryStoreAdapter build(ModelStore store);
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryStoreAdapter.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryStoreAdapter.java
index 1ee02f12..da6d7bd5 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryStoreAdapter.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraModelQueryStoreAdapter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra;
 
 import org.eclipse.viatra.query.runtime.api.ViatraQueryEngineOptions;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraTupleLike.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraTupleLike.java
deleted file mode 100644
index 46c28434..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/ViatraTupleLike.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package tools.refinery.store.query.viatra;
-
-import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
-import tools.refinery.store.tuple.Tuple1;
-import tools.refinery.store.tuple.TupleLike;
-
-public record ViatraTupleLike(ITuple wrappedTuple) implements TupleLike {
-        @Override
-        public int getSize() {
-                return wrappedTuple.getSize();
-        }
-
-        @Override
-        public int get(int element) {
-                var wrappedValue = (Tuple1) wrappedTuple.get(element);
-                return wrappedValue.value0();
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/RelationalScope.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/RelationalScope.java
index 8328e759..d1a65a89 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/RelationalScope.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/RelationalScope.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal;
 
 import org.apache.log4j.Logger;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryAdapterImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryAdapterImpl.java
index 039f46fa..5f3e86b4 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryAdapterImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryAdapterImpl.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal;
 
 import org.eclipse.viatra.query.runtime.api.AdvancedViatraQueryEngine;
@@ -7,62 +12,92 @@ import org.eclipse.viatra.query.runtime.internal.apiimpl.ViatraQueryEngineImpl;
 import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackend;
 import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackendFactory;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.ResultSet;
+import tools.refinery.store.model.ModelListener;
+import tools.refinery.store.query.resultset.AnyResultSet;
+import tools.refinery.store.query.resultset.EmptyResultSet;
+import tools.refinery.store.query.resultset.ResultSet;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.dnf.FunctionalQuery;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.dnf.RelationalQuery;
 import tools.refinery.store.query.viatra.ViatraModelQueryAdapter;
+import tools.refinery.store.query.viatra.internal.matcher.FunctionalViatraMatcher;
+import tools.refinery.store.query.viatra.internal.matcher.RawPatternMatcher;
+import tools.refinery.store.query.viatra.internal.matcher.RelationalViatraMatcher;
 
 import java.lang.invoke.MethodHandle;
 import java.lang.invoke.MethodHandles;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.Map;
 
-public class ViatraModelQueryAdapterImpl implements ViatraModelQueryAdapter {
+public class ViatraModelQueryAdapterImpl implements ViatraModelQueryAdapter, ModelListener {
         private static final String DELAY_MESSAGE_DELIVERY_FIELD_NAME = "delayMessageDelivery";
+        private static final MethodHandle SET_UPDATE_PROPAGATION_DELAYED_HANDLE;
         private static final String QUERY_BACKENDS_FIELD_NAME = "queryBackends";
+        private static final MethodHandle GET_QUERY_BACKENDS_HANDLE;
 
         private final Model model;
         private final ViatraModelQueryStoreAdapterImpl storeAdapter;
         private final ViatraQueryEngineImpl queryEngine;
-        private final MethodHandle setUpdatePropagationDelayedHandle;
-        private final MethodHandle getQueryBackendsHandle;
-        private final Map<DNF, ResultSet> resultSets;
+        private final Map<AnyQuery, AnyResultSet> resultSets;
         private boolean pendingChanges;
 
-        ViatraModelQueryAdapterImpl(Model model, ViatraModelQueryStoreAdapterImpl storeAdapter) {
-                this.model = model;
-                this.storeAdapter = storeAdapter;
-                var scope = new RelationalScope(this);
-                queryEngine = (ViatraQueryEngineImpl) AdvancedViatraQueryEngine.createUnmanagedEngine(scope);
-
+        static {
                 try {
                         var lookup = MethodHandles.privateLookupIn(ViatraQueryEngineImpl.class, MethodHandles.lookup());
-                        setUpdatePropagationDelayedHandle = lookup.findSetter(ViatraQueryEngineImpl.class,
+                        SET_UPDATE_PROPAGATION_DELAYED_HANDLE = lookup.findSetter(ViatraQueryEngineImpl.class,
                                         DELAY_MESSAGE_DELIVERY_FIELD_NAME, Boolean.TYPE);
-                        getQueryBackendsHandle = lookup.findGetter(ViatraQueryEngineImpl.class, QUERY_BACKENDS_FIELD_NAME,
+                        GET_QUERY_BACKENDS_HANDLE = lookup.findGetter(ViatraQueryEngineImpl.class, QUERY_BACKENDS_FIELD_NAME,
                                         Map.class);
                 } catch (IllegalAccessException | NoSuchFieldException e) {
                         throw new IllegalStateException("Cannot access private members of %s"
                                         .formatted(ViatraQueryEngineImpl.class.getName()), e);
                 }
+        }
+
+        ViatraModelQueryAdapterImpl(Model model, ViatraModelQueryStoreAdapterImpl storeAdapter) {
+                this.model = model;
+                this.storeAdapter = storeAdapter;
+                var scope = new RelationalScope(this);
+                queryEngine = (ViatraQueryEngineImpl) AdvancedViatraQueryEngine.createUnmanagedEngine(scope,
+                                storeAdapter.getEngineOptions());
 
                 var querySpecifications = storeAdapter.getQuerySpecifications();
                 GenericQueryGroup.of(
                                 Collections.<IQuerySpecification<?>>unmodifiableCollection(querySpecifications.values()).stream()
                 ).prepare(queryEngine);
-                resultSets = new HashMap<>(querySpecifications.size());
+                var vacuousQueries = storeAdapter.getVacuousQueries();
+                resultSets = new LinkedHashMap<>(querySpecifications.size() + vacuousQueries.size());
                 for (var entry : querySpecifications.entrySet()) {
-                        var matcher = queryEngine.getMatcher(entry.getValue());
-                        resultSets.put(entry.getKey(), matcher);
+                        var rawPatternMatcher = queryEngine.getMatcher(entry.getValue());
+                        var query = entry.getKey();
+                        resultSets.put(query, createResultSet((Query<?>) query, rawPatternMatcher));
+                }
+                for (var vacuousQuery : vacuousQueries) {
+                        resultSets.put(vacuousQuery, new EmptyResultSet<>(this, (Query<?>) vacuousQuery));
                 }
 
                 setUpdatePropagationDelayed(true);
+                model.addListener(this);
+        }
+
+        private <T> ResultSet<T> createResultSet(Query<T> query, RawPatternMatcher matcher) {
+                if (query instanceof RelationalQuery relationalQuery) {
+                        @SuppressWarnings("unchecked")
+                        var resultSet = (ResultSet<T>) new RelationalViatraMatcher(this, relationalQuery, matcher);
+                        return resultSet;
+                } else if (query instanceof FunctionalQuery<T> functionalQuery) {
+                        return new FunctionalViatraMatcher<>(this, functionalQuery, matcher);
+                } else {
+                        throw new IllegalArgumentException("Unknown query: " + query);
+                }
         }
 
         private void setUpdatePropagationDelayed(boolean value) {
                 try {
-                        setUpdatePropagationDelayedHandle.invokeExact(queryEngine, value);
+                        SET_UPDATE_PROPAGATION_DELAYED_HANDLE.invokeExact(queryEngine, value);
                 } catch (Error e) {
                         // Fatal JVM errors should not be wrapped.
                         throw e;
@@ -74,7 +109,7 @@ public class ViatraModelQueryAdapterImpl implements ViatraModelQueryAdapter {
         private Collection<IQueryBackend> getQueryBackends() {
                 try {
                         @SuppressWarnings("unchecked")
-                        var backendMap = (Map<IQueryBackendFactory, IQueryBackend>) getQueryBackendsHandle.invokeExact(queryEngine);
+                        var backendMap = (Map<IQueryBackendFactory, IQueryBackend>) GET_QUERY_BACKENDS_HANDLE.invokeExact(queryEngine);
                         return backendMap.values();
                 } catch (Error e) {
                         // Fatal JVM errors should not be wrapped.
@@ -95,12 +130,14 @@ public class ViatraModelQueryAdapterImpl implements ViatraModelQueryAdapter {
         }
 
         @Override
-        public ResultSet getResultSet(DNF query) {
+        public <T> ResultSet<T> getResultSet(Query<T> query) {
                 var resultSet = resultSets.get(query);
                 if (resultSet == null) {
                         throw new IllegalArgumentException("No matcher for query %s in model".formatted(query.name()));
                 }
-                return resultSet;
+                @SuppressWarnings("unchecked")
+                var typedResultSet = (ResultSet<T>) resultSet;
+                return typedResultSet;
         }
 
         @Override
@@ -132,4 +169,9 @@ public class ViatraModelQueryAdapterImpl implements ViatraModelQueryAdapter {
                 }
                 pendingChanges = false;
         }
+
+        @Override
+        public void afterRestore() {
+                flushChanges();
+        }
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryBuilderImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryBuilderImpl.java
index 9f1e55b1..ce2467b4 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryBuilderImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryBuilderImpl.java
@@ -1,115 +1,162 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal;
 
 import org.eclipse.viatra.query.runtime.api.IQuerySpecification;
 import org.eclipse.viatra.query.runtime.api.ViatraQueryEngineOptions;
-import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchGenericBackendFactory;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchHintOptions;
 import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackendFactory;
 import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
 import org.eclipse.viatra.query.runtime.rete.matcher.ReteBackendFactory;
 import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.DNF;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.dnf.Dnf;
 import tools.refinery.store.query.viatra.ViatraModelQueryBuilder;
-import tools.refinery.store.query.viatra.internal.pquery.DNF2PQuery;
-import tools.refinery.store.query.viatra.internal.pquery.RawPatternMatcher;
+import tools.refinery.store.query.viatra.internal.localsearch.FlatCostFunction;
+import tools.refinery.store.query.viatra.internal.localsearch.RelationalLocalSearchBackendFactory;
+import tools.refinery.store.query.viatra.internal.matcher.RawPatternMatcher;
+import tools.refinery.store.query.viatra.internal.pquery.Dnf2PQuery;
 
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.Map;
+import java.util.*;
 import java.util.function.Function;
 
-public class ViatraModelQueryBuilderImpl extends AbstractModelAdapterBuilder implements ViatraModelQueryBuilder {
+public class ViatraModelQueryBuilderImpl extends AbstractModelAdapterBuilder<ViatraModelQueryStoreAdapterImpl>
+                implements ViatraModelQueryBuilder {
         private ViatraQueryEngineOptions.Builder engineOptionsBuilder;
-        private final DNF2PQuery dnf2PQuery = new DNF2PQuery();
-        private final Map<DNF, IQuerySpecification<RawPatternMatcher>> querySpecifications = new LinkedHashMap<>();
+        private QueryEvaluationHint defaultHint = new QueryEvaluationHint(Map.of(
+                        // Use a cost function that ignores the initial (empty) model but allows higher arity input keys.
+                        LocalSearchHintOptions.PLANNER_COST_FUNCTION, new FlatCostFunction()
+        ), (IQueryBackendFactory) null);
+        private final Dnf2PQuery dnf2PQuery = new Dnf2PQuery();
+        private final Set<AnyQuery> vacuousQueries = new LinkedHashSet<>();
+        private final Map<AnyQuery, IQuerySpecification<RawPatternMatcher>> querySpecifications = new LinkedHashMap<>();
 
-        public ViatraModelQueryBuilderImpl(ModelStoreBuilder storeBuilder) {
-                super(storeBuilder);
+        public ViatraModelQueryBuilderImpl() {
                 engineOptionsBuilder = new ViatraQueryEngineOptions.Builder()
                                 .withDefaultBackend(ReteBackendFactory.INSTANCE)
                                 .withDefaultCachingBackend(ReteBackendFactory.INSTANCE)
-                                .withDefaultSearchBackend(LocalSearchGenericBackendFactory.INSTANCE);
+                                .withDefaultSearchBackend(RelationalLocalSearchBackendFactory.INSTANCE);
         }
 
         @Override
         public ViatraModelQueryBuilder engineOptions(ViatraQueryEngineOptions engineOptions) {
+                checkNotConfigured();
                 engineOptionsBuilder = new ViatraQueryEngineOptions.Builder(engineOptions);
                 return this;
         }
 
         @Override
         public ViatraModelQueryBuilder defaultHint(QueryEvaluationHint queryEvaluationHint) {
-                engineOptionsBuilder.withDefaultHint(queryEvaluationHint);
+                checkNotConfigured();
+                defaultHint = defaultHint.overrideBy(queryEvaluationHint);
                 return this;
         }
 
         @Override
         public ViatraModelQueryBuilder backend(IQueryBackendFactory queryBackendFactory) {
+                checkNotConfigured();
                 engineOptionsBuilder.withDefaultBackend(queryBackendFactory);
                 return this;
         }
 
         @Override
         public ViatraModelQueryBuilder cachingBackend(IQueryBackendFactory queryBackendFactory) {
+                checkNotConfigured();
                 engineOptionsBuilder.withDefaultCachingBackend(queryBackendFactory);
                 return this;
         }
 
         @Override
         public ViatraModelQueryBuilder searchBackend(IQueryBackendFactory queryBackendFactory) {
+                checkNotConfigured();
                 engineOptionsBuilder.withDefaultSearchBackend(queryBackendFactory);
                 return this;
         }
 
         @Override
-        public ViatraModelQueryBuilder query(DNF query) {
-                if (querySpecifications.containsKey(query)) {
-                        throw new IllegalArgumentException("%s was already added to the query engine".formatted(query.name()));
+        public ViatraModelQueryBuilder query(AnyQuery query) {
+                checkNotConfigured();
+                if (querySpecifications.containsKey(query) || vacuousQueries.contains(query)) {
+                        // Ignore duplicate queries.
+                        return this;
+                }
+                var dnf = query.getDnf();
+                var reduction = dnf.getReduction();
+                switch (reduction) {
+                case NOT_REDUCIBLE -> {
+                        var pQuery = dnf2PQuery.translate(dnf);
+                        querySpecifications.put(query, pQuery.build());
+                }
+                case ALWAYS_FALSE -> vacuousQueries.add(query);
+                case ALWAYS_TRUE -> throw new IllegalArgumentException(
+                                "Query %s is relationally unsafe (it matches every tuple)".formatted(query.name()));
+                default -> throw new IllegalArgumentException("Unknown reduction: " + reduction);
                 }
-                var pQuery = dnf2PQuery.translate(query);
-                querySpecifications.put(query, pQuery.build());
                 return this;
         }
 
         @Override
-        public ViatraModelQueryBuilder query(DNF query, QueryEvaluationHint queryEvaluationHint) {
+        public ViatraModelQueryBuilder query(AnyQuery query, QueryEvaluationHint queryEvaluationHint) {
+                hint(query.getDnf(), queryEvaluationHint);
                 query(query);
-                hint(query, queryEvaluationHint);
                 return this;
         }
 
         @Override
-        public ViatraModelQueryBuilder computeHint(Function<DNF, QueryEvaluationHint> computeHint) {
+        public ViatraModelQueryBuilder computeHint(Function<Dnf, QueryEvaluationHint> computeHint) {
+                checkNotConfigured();
                 dnf2PQuery.setComputeHint(computeHint);
                 return this;
         }
 
         @Override
-        public ViatraModelQueryBuilder hint(DNF dnf, QueryEvaluationHint queryEvaluationHint) {
-                var pQuery = dnf2PQuery.getAlreadyTranslated(dnf);
-                if (pQuery == null) {
-                        throw new IllegalArgumentException(
-                                        "Cannot specify hint for %s, because it was not added to the query engine".formatted(dnf.name()));
-                }
-                pQuery.setEvaluationHints(pQuery.getEvaluationHints().overrideBy(queryEvaluationHint));
+        public ViatraModelQueryBuilder hint(Dnf dnf, QueryEvaluationHint queryEvaluationHint) {
+                checkNotConfigured();
+                dnf2PQuery.hint(dnf, queryEvaluationHint);
                 return this;
         }
 
         @Override
-        public ViatraModelQueryStoreAdapterImpl createStoreAdapter(ModelStore store) {
+        public void doConfigure(ModelStoreBuilder storeBuilder) {
+                dnf2PQuery.assertNoUnusedHints();
+        }
+
+        @Override
+        public ViatraModelQueryStoreAdapterImpl doBuild(ModelStore store) {
                 validateSymbols(store);
-                return new ViatraModelQueryStoreAdapterImpl(store, engineOptionsBuilder.build(), dnf2PQuery.getRelationViews(),
-                                Collections.unmodifiableMap(querySpecifications));
+                return new ViatraModelQueryStoreAdapterImpl(store, buildEngineOptions(), dnf2PQuery.getSymbolViews(),
+                                Collections.unmodifiableMap(querySpecifications), Collections.unmodifiableSet(vacuousQueries));
+        }
+
+        private ViatraQueryEngineOptions buildEngineOptions() {
+                // Workaround: manually override the default backend, because {@link ViatraQueryEngineOptions.Builder}
+                // ignores all backend requirements except {@code SPECIFIC}.
+                switch (defaultHint.getQueryBackendRequirementType()) {
+                case SPECIFIC -> engineOptionsBuilder.withDefaultBackend(defaultHint.getQueryBackendFactory());
+                case DEFAULT_CACHING -> engineOptionsBuilder.withDefaultBackend(
+                                engineOptionsBuilder.build().getDefaultCachingBackendFactory());
+                case DEFAULT_SEARCH -> engineOptionsBuilder.withDefaultBackend(
+                                engineOptionsBuilder.build().getDefaultSearchBackendFactory());
+                case UNSPECIFIED -> {
+                        // Nothing to do, leave the default backend unchanged.
+                }
+                }
+                engineOptionsBuilder.withDefaultHint(defaultHint);
+                return engineOptionsBuilder.build();
         }
 
         private void validateSymbols(ModelStore store) {
                 var symbols = store.getSymbols();
-                for (var relationView : dnf2PQuery.getRelationViews().keySet()) {
-                        var symbol = relationView.getSymbol();
+                for (var symbolView : dnf2PQuery.getSymbolViews().keySet()) {
+                        var symbol = symbolView.getSymbol();
                         if (!symbols.contains(symbol)) {
-                                throw new IllegalArgumentException("Cannot query relation view %s: symbol %s is not in the model"
-                                                .formatted(relationView, symbol));
+                                throw new IllegalArgumentException("Cannot query view %s: symbol %s is not in the model"
+                                                .formatted(symbolView, symbol));
                         }
                 }
         }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryStoreAdapterImpl.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryStoreAdapterImpl.java
index 394e407e..11a3c7fd 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryStoreAdapterImpl.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/ViatraModelQueryStoreAdapterImpl.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal;
 
 import org.eclipse.viatra.query.runtime.api.IQuerySpecification;
@@ -5,27 +10,34 @@ import org.eclipse.viatra.query.runtime.api.ViatraQueryEngineOptions;
 import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.DNF;
+import tools.refinery.store.query.dnf.AnyQuery;
 import tools.refinery.store.query.viatra.ViatraModelQueryStoreAdapter;
-import tools.refinery.store.query.viatra.internal.pquery.RawPatternMatcher;
-import tools.refinery.store.query.view.AnyRelationView;
+import tools.refinery.store.query.viatra.internal.matcher.RawPatternMatcher;
+import tools.refinery.store.query.view.AnySymbolView;
 
-import java.util.Collection;
-import java.util.Map;
+import java.util.*;
 
 public class ViatraModelQueryStoreAdapterImpl implements ViatraModelQueryStoreAdapter {
         private final ModelStore store;
         private final ViatraQueryEngineOptions engineOptions;
-        private final Map<AnyRelationView, IInputKey> inputKeys;
-        private final Map<DNF, IQuerySpecification<RawPatternMatcher>> querySpecifications;
+        private final Map<AnySymbolView, IInputKey> inputKeys;
+        private final Map<AnyQuery, IQuerySpecification<RawPatternMatcher>> querySpecifications;
+        private final Set<AnyQuery> vacuousQueries;
+        private final Set<AnyQuery> allQueries;
 
         ViatraModelQueryStoreAdapterImpl(ModelStore store, ViatraQueryEngineOptions engineOptions,
-                                                                         Map<AnyRelationView, IInputKey> inputKeys,
-                                                                         Map<DNF, IQuerySpecification<RawPatternMatcher>> querySpecifications) {
+                                                                         Map<AnySymbolView, IInputKey> inputKeys,
+                                                                         Map<AnyQuery, IQuerySpecification<RawPatternMatcher>> querySpecifications,
+                                                                         Set<AnyQuery> vacuousQueries) {
                 this.store = store;
                 this.engineOptions = engineOptions;
                 this.inputKeys = inputKeys;
                 this.querySpecifications = querySpecifications;
+                this.vacuousQueries = vacuousQueries;
+                var mutableAllQueries = new LinkedHashSet<AnyQuery>(querySpecifications.size() + vacuousQueries.size());
+                mutableAllQueries.addAll(querySpecifications.keySet());
+                mutableAllQueries.addAll(vacuousQueries);
+                this.allQueries = Collections.unmodifiableSet(mutableAllQueries);
         }
 
         @Override
@@ -33,23 +45,27 @@ public class ViatraModelQueryStoreAdapterImpl implements ViatraModelQueryStoreAd
                 return store;
         }
 
-        public Collection<AnyRelationView> getRelationViews() {
+        public Collection<AnySymbolView> getSymbolViews() {
                 return inputKeys.keySet();
         }
 
-        public Map<AnyRelationView, IInputKey> getInputKeys() {
+        public Map<AnySymbolView, IInputKey> getInputKeys() {
                 return inputKeys;
         }
 
         @Override
-        public Collection<DNF> getQueries() {
-                return querySpecifications.keySet();
+        public Collection<AnyQuery> getQueries() {
+                return allQueries;
         }
 
-        Map<DNF, IQuerySpecification<RawPatternMatcher>> getQuerySpecifications() {
+        Map<AnyQuery, IQuerySpecification<RawPatternMatcher>> getQuerySpecifications() {
                 return querySpecifications;
         }
 
+        Set<AnyQuery> getVacuousQueries() {
+                return vacuousQueries;
+        }
+
         @Override
         public ViatraQueryEngineOptions getEngineOptions() {
                 return engineOptions;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperator.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperator.java
deleted file mode 100644
index e0bca9e0..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperator.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package tools.refinery.store.query.viatra.internal.cardinality;
-
-import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.BoundAggregator;
-import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.IMultisetAggregationOperator;
-import tools.refinery.store.representation.cardinality.FiniteUpperCardinality;
-import tools.refinery.store.representation.cardinality.UnboundedUpperCardinality;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import java.util.stream.Stream;
-
-public class UpperCardinalitySumAggregationOperator implements IMultisetAggregationOperator<UpperCardinality,
-                UpperCardinalitySumAggregationOperator.Accumulator, UpperCardinality> {
-        public static final UpperCardinalitySumAggregationOperator INSTANCE = new UpperCardinalitySumAggregationOperator();
-
-        public static final BoundAggregator BOUND_AGGREGATOR = new BoundAggregator(INSTANCE, UpperCardinality.class,
-                        UpperCardinality.class);
-
-        private UpperCardinalitySumAggregationOperator() {
-                // Singleton constructor.
-        }
-
-        @Override
-        public String getName() {
-                return "sum<UpperCardinality>";
-        }
-
-        @Override
-        public String getShortDescription() {
-                return "%s computes the sum of finite or unbounded upper cardinalities".formatted(getName());
-        }
-
-        @Override
-        public Accumulator createNeutral() {
-                return new Accumulator();
-        }
-
-        @Override
-        public boolean isNeutral(Accumulator result) {
-                return result.sumFiniteUpperBounds == 0 && result.countUnbounded == 0;
-        }
-
-        @Override
-        public Accumulator update(Accumulator oldResult, UpperCardinality updateValue, boolean isInsertion) {
-                if (updateValue instanceof FiniteUpperCardinality finiteUpperCardinality) {
-                        int finiteUpperBound = finiteUpperCardinality.finiteUpperBound();
-                        if (isInsertion) {
-                                oldResult.sumFiniteUpperBounds += finiteUpperBound;
-                        } else {
-                                oldResult.sumFiniteUpperBounds -= finiteUpperBound;
-                        }
-                } else if (updateValue instanceof UnboundedUpperCardinality) {
-                        if (isInsertion) {
-                                oldResult.countUnbounded += 1;
-                        } else {
-                                oldResult.countUnbounded -= 1;
-                        }
-                } else {
-                        throw new IllegalArgumentException("Unknown UpperCardinality: " + updateValue);
-                }
-                return oldResult;
-        }
-
-        @Override
-        public UpperCardinality getAggregate(Accumulator result) {
-                return result.countUnbounded > 0 ? UpperCardinalities.UNBOUNDED :
-                                UpperCardinalities.valueOf(result.sumFiniteUpperBounds);
-        }
-
-        @Override
-        public UpperCardinality aggregateStream(Stream<UpperCardinality> stream) {
-                var result = stream.collect(this::createNeutral, (accumulator, value) -> update(accumulator, value, true),
-                                (left, right) -> new Accumulator(left.sumFiniteUpperBounds + right.sumFiniteUpperBounds,
-                                                left.countUnbounded + right.countUnbounded));
-                return getAggregate(result);
-        }
-
-        @Override
-        public Accumulator clone(Accumulator original) {
-                return new Accumulator(original.sumFiniteUpperBounds, original.countUnbounded);
-        }
-
-        public static class Accumulator {
-                private int sumFiniteUpperBounds;
-
-                private int countUnbounded;
-
-                private Accumulator(int sumFiniteUpperBounds, int countUnbounded) {
-                        this.sumFiniteUpperBounds = sumFiniteUpperBounds;
-                        this.countUnbounded = countUnbounded;
-                }
-
-                private Accumulator() {
-                        this(0, 0);
-                }
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/DummyBaseIndexer.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/DummyBaseIndexer.java
index 2a24b67c..8cb199d2 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/DummyBaseIndexer.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/DummyBaseIndexer.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.context;
 
 import org.eclipse.viatra.query.runtime.api.scope.IBaseIndex;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalEngineContext.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalEngineContext.java
index 28bc69d0..7220f8ca 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalEngineContext.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalEngineContext.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.context;
 
 import org.eclipse.viatra.query.runtime.api.scope.IBaseIndex;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalQueryMetaContext.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalQueryMetaContext.java
index cba3fa08..211eacb4 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalQueryMetaContext.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalQueryMetaContext.java
@@ -1,10 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.context;
 
 import org.eclipse.viatra.query.runtime.matchers.context.AbstractQueryMetaContext;
 import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
 import org.eclipse.viatra.query.runtime.matchers.context.InputKeyImplication;
-import tools.refinery.store.query.viatra.internal.pquery.RelationViewWrapper;
-import tools.refinery.store.query.view.AnyRelationView;
+import org.eclipse.viatra.query.runtime.matchers.context.common.JavaTransitiveInstancesKey;
+import tools.refinery.store.query.viatra.internal.pquery.SymbolViewWrapper;
+import tools.refinery.store.query.view.AnySymbolView;
 
 import java.util.*;
 
@@ -12,9 +18,9 @@ import java.util.*;
  * The meta context information for String scopes.
  */
 public class RelationalQueryMetaContext extends AbstractQueryMetaContext {
-        private final Map<AnyRelationView, IInputKey> inputKeys;
+        private final Map<AnySymbolView, IInputKey> inputKeys;
 
-        RelationalQueryMetaContext(Map<AnyRelationView, IInputKey> inputKeys) {
+        RelationalQueryMetaContext(Map<AnySymbolView, IInputKey> inputKeys) {
                 this.inputKeys = inputKeys;
         }
 
@@ -37,26 +43,43 @@ public class RelationalQueryMetaContext extends AbstractQueryMetaContext {
 
         @Override
         public Collection<InputKeyImplication> getImplications(IInputKey implyingKey) {
-                var relationView = checkKey(implyingKey);
-                var relationViewImplications = relationView.getImpliedRelationViews();
+                if (implyingKey instanceof JavaTransitiveInstancesKey) {
+                        return List.of();
+                }
+                var symbolView = checkKey(implyingKey);
+                var relationViewImplications = symbolView.getImpliedRelationViews();
                 var inputKeyImplications = new HashSet<InputKeyImplication>(relationViewImplications.size());
                 for (var relationViewImplication : relationViewImplications) {
-                        if (!relationView.equals(relationViewImplication.implyingRelationView())) {
+                        if (!symbolView.equals(relationViewImplication.implyingView())) {
                                 throw new IllegalArgumentException("Relation view %s returned unrelated implication %s".formatted(
-                                                relationView, relationViewImplication));
+                                                symbolView, relationViewImplication));
                         }
-                        var impliedInputKey = inputKeys.get(relationViewImplication.impliedRelationView());
+                        var impliedInputKey = inputKeys.get(relationViewImplication.impliedView());
                         // Ignore implications not relevant for any queries included in the model.
                         if (impliedInputKey != null) {
                                 inputKeyImplications.add(new InputKeyImplication(implyingKey, impliedInputKey,
                                                 relationViewImplication.impliedIndices()));
                         }
                 }
+                var parameters = symbolView.getParameters();
+                int arity = symbolView.arity();
+                for (int i = 0; i < arity; i++) {
+                        var parameter = parameters.get(i);
+                        var parameterType = parameter.tryGetType();
+                        if (parameterType.isPresent()) {
+                                var javaTransitiveInstancesKey = new JavaTransitiveInstancesKey(parameterType.get());
+                                var javaImplication = new InputKeyImplication(implyingKey, javaTransitiveInstancesKey, List.of(i));
+                                inputKeyImplications.add(javaImplication);
+                        }
+                }
                 return inputKeyImplications;
         }
 
         @Override
         public Map<Set<Integer>, Set<Integer>> getFunctionalDependencies(IInputKey key) {
+                if (key instanceof JavaTransitiveInstancesKey) {
+                        return Map.of();
+                }
                 var relationView = checkKey(key);
                 var functionalDependencies = relationView.getFunctionalDependencies();
                 var flattened = new HashMap<Set<Integer>, Set<Integer>>(functionalDependencies.size());
@@ -75,20 +98,20 @@ public class RelationalQueryMetaContext extends AbstractQueryMetaContext {
                 return flattened;
         }
 
-        private static void checkValidIndices(AnyRelationView relationView, Collection<Integer> indices) {
+        private static void checkValidIndices(AnySymbolView relationView, Collection<Integer> indices) {
                 indices.stream().filter(relationView::invalidIndex).findAny().ifPresent(i -> {
                         throw new IllegalArgumentException("Index %d is invalid for %s".formatted(i, relationView));
                 });
         }
 
-        public AnyRelationView checkKey(IInputKey key) {
-                if (!(key instanceof RelationViewWrapper wrapper)) {
+        public AnySymbolView checkKey(IInputKey key) {
+                if (!(key instanceof SymbolViewWrapper wrapper)) {
                         throw new IllegalArgumentException("The input key %s is not a valid input key".formatted(key));
                 }
-                var relationView = wrapper.getWrappedKey();
-                if (!inputKeys.containsKey(relationView)) {
+                var symbolView = wrapper.getWrappedKey();
+                if (!inputKeys.containsKey(symbolView)) {
                         throw new IllegalArgumentException("The input key %s is not present in the model".formatted(key));
                 }
-                return relationView;
+                return symbolView;
         }
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalRuntimeContext.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalRuntimeContext.java
index 01d20d3e..0f2daca8 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalRuntimeContext.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/context/RelationalRuntimeContext.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.context;
 
 import org.eclipse.viatra.query.runtime.matchers.context.*;
@@ -8,9 +13,9 @@ import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
 import org.eclipse.viatra.query.runtime.matchers.util.Accuracy;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
-import tools.refinery.store.query.viatra.internal.pquery.RelationViewWrapper;
+import tools.refinery.store.query.viatra.internal.pquery.SymbolViewWrapper;
 import tools.refinery.store.query.viatra.internal.update.ModelUpdateListener;
-import tools.refinery.store.query.view.AnyRelationView;
+import tools.refinery.store.query.view.AnySymbolView;
 
 import java.lang.reflect.InvocationTargetException;
 import java.util.Iterator;
@@ -54,8 +59,9 @@ public class RelationalRuntimeContext implements IQueryRuntimeContext {
 
         @Override
         public boolean isIndexed(IInputKey key, IndexingService service) {
-                if (key instanceof AnyRelationView relationalKey) {
-                        return this.modelUpdateListener.containsRelationView(relationalKey);
+                if (key instanceof SymbolViewWrapper wrapper) {
+                        var symbolViewKey = wrapper.getWrappedKey();
+                        return this.modelUpdateListener.containsSymbolView(symbolViewKey);
                 } else {
                         return false;
                 }
@@ -68,13 +74,13 @@ public class RelationalRuntimeContext implements IQueryRuntimeContext {
                 }
         }
 
-        AnyRelationView checkKey(IInputKey key) {
-                if (key instanceof RelationViewWrapper wrappedKey) {
-                        var relationViewKey = wrappedKey.getWrappedKey();
-                        if (modelUpdateListener.containsRelationView(relationViewKey)) {
-                                return relationViewKey;
+        AnySymbolView checkKey(IInputKey key) {
+                if (key instanceof SymbolViewWrapper wrappedKey) {
+                        var symbolViewKey = wrappedKey.getWrappedKey();
+                        if (modelUpdateListener.containsSymbolView(symbolViewKey)) {
+                                return symbolViewKey;
                         } else {
-                                throw new IllegalStateException("Query is asking for non-indexed key %s".formatted(relationViewKey));
+                                throw new IllegalStateException("Query is asking for non-indexed key %s".formatted(symbolViewKey));
                         }
                 } else {
                         throw new IllegalStateException("Query is asking for non-relational key");
@@ -83,10 +89,7 @@ public class RelationalRuntimeContext implements IQueryRuntimeContext {
 
         @Override
         public int countTuples(IInputKey key, TupleMask seedMask, ITuple seed) {
-                var relationViewKey = checkKey(key);
-                Iterable<Object[]> allObjects = relationViewKey.getAll(model);
-                Iterable<Object[]> filteredBySeed = filter(allObjects, objectArray -> isMatching(objectArray, seedMask, seed));
-                Iterator<Object[]> iterator = filteredBySeed.iterator();
+                Iterator<Object[]> iterator = enumerate(key, seedMask, seed).iterator();
                 int result = 0;
                 while (iterator.hasNext()) {
                         iterator.next();
@@ -102,13 +105,25 @@ public class RelationalRuntimeContext implements IQueryRuntimeContext {
 
         @Override
         public Iterable<Tuple> enumerateTuples(IInputKey key, TupleMask seedMask, ITuple seed) {
+                var filteredBySeed = enumerate(key, seedMask, seed);
+                return map(filteredBySeed, Tuples::flatTupleOf);
+        }
+
+        @Override
+        public Iterable<?> enumerateValues(IInputKey key, TupleMask seedMask, ITuple seed) {
+                var index = seedMask.getFirstOmittedIndex().orElseThrow(
+                                () -> new IllegalArgumentException("Seed mask does not omit a value"));
+                var filteredBySeed = enumerate(key, seedMask, seed);
+                return map(filteredBySeed, array -> array[index]);
+        }
+
+        private Iterable<Object[]> enumerate(IInputKey key, TupleMask seedMask, ITuple seed) {
                 var relationViewKey = checkKey(key);
                 Iterable<Object[]> allObjects = relationViewKey.getAll(model);
-                Iterable<Object[]> filteredBySeed = filter(allObjects, objectArray -> isMatching(objectArray, seedMask, seed));
-                return map(filteredBySeed, Tuples::flatTupleOf);
+                return filter(allObjects, objectArray -> isMatching(objectArray, seedMask, seed));
         }
 
-        private boolean isMatching(Object[] tuple, TupleMask seedMask, ITuple seed) {
+        private static boolean isMatching(Object[] tuple, TupleMask seedMask, ITuple seed) {
                 for (int i = 0; i < seedMask.indices.length; i++) {
                         final Object seedElement = seed.get(i);
                         final Object tupleElement = tuple[seedMask.indices[i]];
@@ -120,11 +135,6 @@ public class RelationalRuntimeContext implements IQueryRuntimeContext {
         }
 
         @Override
-        public Iterable<?> enumerateValues(IInputKey key, TupleMask seedMask, ITuple seed) {
-                return enumerateTuples(key, seedMask, seed);
-        }
-
-        @Override
         public boolean containsTuple(IInputKey key, ITuple seed) {
                 var relationViewKey = checkKey(key);
                 return relationViewKey.get(model, seed.getElements());
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendOperationExecutor.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendOperationExecutor.java
new file mode 100644
index 00000000..37177cbf
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendOperationExecutor.java
@@ -0,0 +1,76 @@
+/*******************************************************************************
+ * Copyright (c) 2010-2013, Zoltan Ujhelyi, Akos Horvath, Istvan Rath and Daniel Varro
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Public License v. 2.0 which is available at
+ * http://www.eclipse.org/legal/epl-v20.html.
+ * SPDX-License-Identifier: EPL-2.0
+ *******************************************************************************/
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.MatchingFrame;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.ISearchContext;
+import org.eclipse.viatra.query.runtime.localsearch.operations.ISearchOperation.ISearchOperationExecutor;
+
+import java.util.Iterator;
+
+/**
+ * An operation that can be used to enumerate all possible values for a single position based on a constraint
+ * @author Zoltan Ujhelyi, Akos Horvath
+ * @since 2.0
+ */
+abstract class ExtendOperationExecutor<T> implements ISearchOperationExecutor {
+
+    private Iterator<? extends T> it;
+
+    /**
+     * Returns an iterator with the possible options from the current state
+     * @since 2.0
+     */
+        @SuppressWarnings("squid:S1452")
+    protected abstract Iterator<? extends T> getIterator(MatchingFrame frame, ISearchContext context);
+    /**
+     * Updates the frame with the next element of the iterator. Called during {@link #execute(MatchingFrame, ISearchContext)}.
+     *
+     * @return true if the update is successful or false otherwise; in case of false is returned, the next element should be taken from the iterator.
+     * @since 2.0
+     */
+    protected abstract boolean fillInValue(T newValue, MatchingFrame frame, ISearchContext context);
+
+    /**
+     * Restores the frame to the state before {@link #fillInValue(Object, MatchingFrame, ISearchContext)}. Called during
+     * {@link #onBacktrack(MatchingFrame, ISearchContext)}.
+     *
+     * @since 2.0
+     */
+    protected abstract void cleanup(MatchingFrame frame, ISearchContext context);
+
+    @Override
+    public void onInitialize(MatchingFrame frame, ISearchContext context) {
+        it = getIterator(frame, context);
+    }
+
+    @Override
+    public void onBacktrack(MatchingFrame frame, ISearchContext context) {
+        it = null;
+
+    }
+
+        /**
+         * Fixed version of {@link org.eclipse.viatra.query.runtime.localsearch.operations.ExtendOperationExecutor#execute}
+         * that handles failed unification of variables correctly.
+         * @param frame The matching frame to extend.
+         * @param context The search context.
+         * @return {@code true} if an extension was found, {@code false} otherwise.
+         */
+    @Override
+    public boolean execute(MatchingFrame frame, ISearchContext context) {
+                while (it.hasNext()) {
+                        var newValue = it.next();
+                        if (fillInValue(newValue, frame, context)) {
+                                return true;
+                        }
+                }
+                return false;
+    }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendPositivePatternCall.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendPositivePatternCall.java
new file mode 100644
index 00000000..9d48c785
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/ExtendPositivePatternCall.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (c) 2010-2016, Grill Balázs, IncQueryLabs
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Public License v. 2.0 which is available at
+ * http://www.eclipse.org/legal/epl-v20.html.
+ * SPDX-License-Identifier: EPL-2.0
+ *******************************************************************************/
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.MatchingFrame;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.ISearchContext;
+import org.eclipse.viatra.query.runtime.localsearch.operations.IPatternMatcherOperation;
+import org.eclipse.viatra.query.runtime.localsearch.operations.ISearchOperation;
+import org.eclipse.viatra.query.runtime.localsearch.operations.util.CallInformation;
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryResultProvider;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.matchers.tuple.VolatileModifiableMaskedTuple;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.function.Function;
+
+/**
+ * @author Grill Balázs
+ * @since 1.4
+ *
+ */
+public class ExtendPositivePatternCall implements ISearchOperation, IPatternMatcherOperation {
+
+    private class Executor extends ExtendOperationExecutor<Tuple> {
+        private final VolatileModifiableMaskedTuple maskedTuple;
+
+        public Executor() {
+            maskedTuple = new VolatileModifiableMaskedTuple(information.getThinFrameMask());
+        }
+
+        @Override
+        protected Iterator<? extends Tuple> getIterator(MatchingFrame frame, ISearchContext context) {
+            maskedTuple.updateTuple(frame);
+            IQueryResultProvider matcher = context.getMatcher(information.getCallWithAdornment());
+            return matcher.getAllMatches(information.getParameterMask(), maskedTuple).iterator();
+        }
+
+        /**
+         * @since 2.0
+         */
+        @Override
+        protected boolean fillInValue(Tuple result, MatchingFrame frame, ISearchContext context) {
+            TupleMask mask = information.getFullFrameMask();
+            // The first loop clears out the elements from a possible previous iteration
+            for(int i : information.getFreeParameterIndices()) {
+                mask.set(frame, i, null);
+            }
+            for(int i : information.getFreeParameterIndices()) {
+                Object oldValue = mask.getValue(frame, i);
+                Object valueToFill = result.get(i);
+                if (oldValue != null && !oldValue.equals(valueToFill)){
+                    // If the inverse map contains more than one values for the same key, it means that these arguments are unified by the caller.
+                    // In this case if the callee assigns different values the frame shall be dropped
+                    return false;
+                }
+                mask.set(frame, i, valueToFill);
+            }
+            return true;
+        }
+
+        @Override
+        protected void cleanup(MatchingFrame frame, ISearchContext context) {
+            TupleMask mask = information.getFullFrameMask();
+            for(int i : information.getFreeParameterIndices()){
+                mask.set(frame, i, null);
+            }
+
+        }
+
+        @Override
+        public ISearchOperation getOperation() {
+            return ExtendPositivePatternCall.this;
+        }
+    }
+
+    private final CallInformation information;
+
+    /**
+     * @since 1.7
+     */
+    public ExtendPositivePatternCall(CallInformation information) {
+       this.information = information;
+    }
+
+    @Override
+    public ISearchOperationExecutor createExecutor() {
+        return new Executor();
+    }
+
+    @Override
+    public List<Integer> getVariablePositions() {
+        return information.getVariablePositions();
+    }
+
+    @Override
+    public String toString() {
+        return toString(Object::toString);
+    }
+
+    @Override
+    public String toString(@SuppressWarnings("squid:S4276") Function<Integer, String> variableMapping) {
+        return "extend find " + information.toString(variableMapping);
+    }
+
+    @Override
+    public CallInformation getCallInformation() {
+        return information;
+    }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/FlatCostFunction.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/FlatCostFunction.java
new file mode 100644
index 00000000..cc906f22
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/FlatCostFunction.java
@@ -0,0 +1,35 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.planner.cost.IConstraintEvaluationContext;
+import org.eclipse.viatra.query.runtime.localsearch.planner.cost.impl.StatisticsBasedConstraintCostFunction;
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.TypeConstraint;
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.matchers.util.Accuracy;
+
+import java.util.Optional;
+
+public class FlatCostFunction extends StatisticsBasedConstraintCostFunction {
+        public FlatCostFunction() {
+                // No inverse navigation penalty thanks to relational storage.
+                super(0);
+        }
+
+        @Override
+        public Optional<Long> projectionSize(IConstraintEvaluationContext input, IInputKey supplierKey, TupleMask groupMask, Accuracy requiredAccuracy) {
+                // We always start from an empty model, where every projection is of size 0.
+                // Therefore, projection size estimation is meaningless.
+                return Optional.empty();
+        }
+
+        @Override
+        protected double _calculateCost(TypeConstraint constraint, IConstraintEvaluationContext input) {
+                // Assume a flat cost for each relation. Maybe adjust in the future if we perform indexing?
+                return DEFAULT_COST;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/GenericTypeExtend.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/GenericTypeExtend.java
new file mode 100644
index 00000000..96ac4a72
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/GenericTypeExtend.java
@@ -0,0 +1,137 @@
+/*******************************************************************************
+ * Copyright (c) 2010-2017, Zoltan Ujhelyi, IncQuery Labs Ltd.
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Public License v. 2.0 which is available at
+ * http://www.eclipse.org/legal/epl-v20.html.
+ * SPDX-License-Identifier: EPL-2.0
+ *******************************************************************************/
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.MatchingFrame;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.ISearchContext;
+import org.eclipse.viatra.query.runtime.localsearch.operations.IIteratingSearchOperation;
+import org.eclipse.viatra.query.runtime.localsearch.operations.ISearchOperation;
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.matchers.tuple.VolatileMaskedTuple;
+import org.eclipse.viatra.query.runtime.matchers.util.Preconditions;
+
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+/**
+ * @author Zoltan Ujhelyi
+ * @since 1.7
+ */
+public class GenericTypeExtend implements IIteratingSearchOperation {
+    private class Executor extends ExtendOperationExecutor<Tuple> {
+        private final VolatileMaskedTuple maskedTuple;
+
+        public Executor() {
+            this.maskedTuple = new VolatileMaskedTuple(callMask);
+        }
+
+        @Override
+        protected Iterator<? extends Tuple> getIterator(MatchingFrame frame, ISearchContext context) {
+            maskedTuple.updateTuple(frame);
+            return context.getRuntimeContext().enumerateTuples(type, indexerMask, maskedTuple).iterator();
+        }
+
+        @Override
+        protected boolean fillInValue(Tuple newTuple, MatchingFrame frame, ISearchContext context) {
+            for (Integer position : unboundVariableIndices) {
+                frame.setValue(position, null);
+            }
+            for (int i = 0; i < positions.length; i++) {
+                Object newValue = newTuple.get(i);
+                Object oldValue = frame.getValue(positions[i]);
+                if (oldValue != null && !Objects.equals(oldValue, newValue)) {
+                    // If positions tuple maps more than one values for the same element (e.g. loop), it means that
+                    // these arguments are to unified by the caller. In this case if the callee assigns different values
+                    // the frame shall be considered a failed match
+                    return false;
+                }
+                frame.setValue(positions[i], newValue);
+            }
+            return true;
+        }
+
+        @Override
+        protected void cleanup(MatchingFrame frame, ISearchContext context) {
+            for (Integer position : unboundVariableIndices) {
+                frame.setValue(position, null);
+            }
+        }
+
+                @Override
+        public ISearchOperation getOperation() {
+            return GenericTypeExtend.this;
+        }
+    }
+
+    private final IInputKey type;
+    private final int[] positions;
+    private final List<Integer> positionList;
+    private final Set<Integer> unboundVariableIndices;
+    private final TupleMask indexerMask;
+    private final TupleMask callMask;
+
+    /**
+     *
+     * @param type
+     *            the type to execute the extend operation on
+     * @param positions
+     *            the parameter positions that represent the variables of the input key
+     * @param unboundVariableIndices
+     *            the set of positions that are bound at the start of the operation
+     */
+    public GenericTypeExtend(IInputKey type, int[] positions, TupleMask callMask, TupleMask indexerMask, Set<Integer> unboundVariableIndices) {
+        Preconditions.checkArgument(positions.length == type.getArity(),
+                "The type %s requires %d parameters, but %d positions are provided", type.getPrettyPrintableName(),
+                type.getArity(), positions.length);
+        List<Integer> modifiablePositionList = new ArrayList<>();
+        for (int position : positions) {
+            modifiablePositionList.add(position);
+        }
+        this.positionList = Collections.unmodifiableList(modifiablePositionList);
+        this.positions = positions;
+        this.type = type;
+
+        this.unboundVariableIndices = unboundVariableIndices;
+        this.indexerMask = indexerMask;
+        this.callMask = callMask;
+    }
+
+    @Override
+    public IInputKey getIteratedInputKey() {
+        return type;
+    }
+
+    @Override
+    public ISearchOperationExecutor createExecutor() {
+        return new Executor();
+    }
+
+    @Override
+    public List<Integer> getVariablePositions() {
+        return positionList;
+    }
+
+    @Override
+    public String toString() {
+        return toString(Object::toString);
+    }
+
+    @Override
+    public String toString(@SuppressWarnings("squid:S4276") Function<Integer, String> variableMapping) {
+        return "extend    " + type.getPrettyPrintableName() + "("
+                + positionList.stream()
+                        .map(input -> String.format("%s%s", unboundVariableIndices.contains(input) ? "-" : "+", variableMapping.apply(input)))
+                        .collect(Collectors.joining(", "))
+                + ")";
+    }
+
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchBackendFactory.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchBackendFactory.java
new file mode 100644
index 00000000..0c77f587
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchBackendFactory.java
@@ -0,0 +1,60 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.AbstractLocalSearchResultProvider;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchBackend;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchHints;
+import org.eclipse.viatra.query.runtime.localsearch.plan.IPlanProvider;
+import org.eclipse.viatra.query.runtime.localsearch.plan.SimplePlanProvider;
+import org.eclipse.viatra.query.runtime.matchers.backend.IMatcherCapability;
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackend;
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackendFactory;
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import org.eclipse.viatra.query.runtime.matchers.context.IQueryBackendContext;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PQuery;
+
+public class RelationalLocalSearchBackendFactory implements IQueryBackendFactory {
+        public static final RelationalLocalSearchBackendFactory INSTANCE = new RelationalLocalSearchBackendFactory();
+
+        private RelationalLocalSearchBackendFactory() {
+        }
+
+        @Override
+        public IQueryBackend create(IQueryBackendContext context) {
+                return new LocalSearchBackend(context) {
+                        // Create a new {@link IPlanProvider}, because the original {@link LocalSearchBackend#planProvider} is not
+                        // accessible.
+                        private final IPlanProvider planProvider = new SimplePlanProvider(context.getLogger());
+
+                        @Override
+                        protected AbstractLocalSearchResultProvider initializeResultProvider(PQuery query,
+                                                                                                                                                                 QueryEvaluationHint hints) {
+                                return new RelationalLocalSearchResultProvider(this, context, query, planProvider, hints);
+                        }
+
+                        @Override
+                        public IQueryBackendFactory getFactory() {
+                                return RelationalLocalSearchBackendFactory.this;
+                        }
+                };
+        }
+
+        @Override
+        public Class<? extends IQueryBackend> getBackendClass() {
+                return LocalSearchBackend.class;
+        }
+
+        @Override
+        public IMatcherCapability calculateRequiredCapability(PQuery pQuery, QueryEvaluationHint queryEvaluationHint) {
+                return LocalSearchHints.parse(queryEvaluationHint);
+        }
+
+        @Override
+        public boolean isCaching() {
+                return false;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchResultProvider.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchResultProvider.java
new file mode 100644
index 00000000..da37be14
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalLocalSearchResultProvider.java
@@ -0,0 +1,28 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.AbstractLocalSearchResultProvider;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchBackend;
+import org.eclipse.viatra.query.runtime.localsearch.matcher.integration.LocalSearchHints;
+import org.eclipse.viatra.query.runtime.localsearch.plan.IPlanProvider;
+import org.eclipse.viatra.query.runtime.localsearch.planner.compiler.IOperationCompiler;
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import org.eclipse.viatra.query.runtime.matchers.context.IQueryBackendContext;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PQuery;
+
+class RelationalLocalSearchResultProvider extends AbstractLocalSearchResultProvider {
+        public RelationalLocalSearchResultProvider(LocalSearchBackend backend, IQueryBackendContext context, PQuery query,
+                                                                                           IPlanProvider planProvider, QueryEvaluationHint userHints) {
+                super(backend, context, query, planProvider, userHints);
+        }
+
+        @Override
+        protected IOperationCompiler getOperationCompiler(IQueryBackendContext backendContext,
+                                                                                                          LocalSearchHints configuration) {
+                return new RelationalOperationCompiler(runtimeContext);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalOperationCompiler.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalOperationCompiler.java
new file mode 100644
index 00000000..f76ef486
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/localsearch/RelationalOperationCompiler.java
@@ -0,0 +1,70 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.localsearch;
+
+import org.eclipse.viatra.query.runtime.localsearch.operations.generic.GenericTypeExtendSingleValue;
+import org.eclipse.viatra.query.runtime.localsearch.operations.util.CallInformation;
+import org.eclipse.viatra.query.runtime.localsearch.planner.compiler.GenericOperationCompiler;
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContext;
+import org.eclipse.viatra.query.runtime.matchers.psystem.PVariable;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.PositivePatternCall;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.TypeConstraint;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+
+import java.util.*;
+
+public class RelationalOperationCompiler extends GenericOperationCompiler  {
+        public RelationalOperationCompiler(IQueryRuntimeContext runtimeContext) {
+                super(runtimeContext);
+        }
+
+        @Override
+        protected void createExtend(TypeConstraint typeConstraint, Map<PVariable, Integer> variableMapping) {
+                IInputKey inputKey = typeConstraint.getSupplierKey();
+                Tuple tuple = typeConstraint.getVariablesTuple();
+
+                int[] positions = new int[tuple.getSize()];
+                List<Integer> boundVariableIndices = new ArrayList<>();
+                List<Integer> boundVariables = new ArrayList<>();
+                Set<Integer> unboundVariables = new HashSet<>();
+                for (int i = 0; i < tuple.getSize(); i++) {
+                        PVariable variable = (PVariable) tuple.get(i);
+                        Integer position = variableMapping.get(variable);
+                        positions[i] = position;
+                        if (variableBindings.get(typeConstraint).contains(position)) {
+                                boundVariableIndices.add(i);
+                                boundVariables.add(position);
+                        } else {
+                                unboundVariables.add(position);
+                        }
+                }
+                TupleMask indexerMask = TupleMask.fromSelectedIndices(inputKey.getArity(), boundVariableIndices);
+                TupleMask callMask = TupleMask.fromSelectedIndices(variableMapping.size(), boundVariables);
+                // If multiple tuple elements from the indexer should be bound to the same variable, we must use a
+                // {@link GenericTypeExtend} check whether the tuple elements have the same value.
+                if (unboundVariables.size() == 1 && indexerMask.getSize() + 1 == indexerMask.getSourceWidth()) {
+                        operations.add(new GenericTypeExtendSingleValue(inputKey, positions, callMask, indexerMask,
+                                        unboundVariables.iterator().next()));
+                } else {
+                        // Use a fixed version of
+                        // {@code org.eclipse.viatra.query.runtime.localsearch.operations.generic.GenericTypeExtend} that handles
+                        // failed unification of variables correctly.
+                        operations.add(new GenericTypeExtend(inputKey, positions, callMask, indexerMask, unboundVariables));
+                }
+        }
+
+        @Override
+        protected void createExtend(PositivePatternCall pCall, Map<PVariable, Integer> variableMapping) {
+                CallInformation information = CallInformation.create(pCall, variableMapping, variableBindings.get(pCall));
+                // Use a fixed version of
+                // {@code org.eclipse.viatra.query.runtime.localsearch.operations.extend.ExtendPositivePatternCall} that handles
+                // failed unification of variables correctly.
+                operations.add(new ExtendPositivePatternCall(information));
+                dependencies.add(information.getCallWithAdornment());
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/AbstractViatraMatcher.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/AbstractViatraMatcher.java
new file mode 100644
index 00000000..99b0a3d8
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/AbstractViatraMatcher.java
@@ -0,0 +1,32 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryResultProvider;
+import org.eclipse.viatra.query.runtime.matchers.backend.IUpdateable;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.resultset.AbstractResultSet;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
+
+public abstract class AbstractViatraMatcher<T> extends AbstractResultSet<T> implements IUpdateable {
+        protected final IQueryResultProvider backend;
+
+        protected AbstractViatraMatcher(ViatraModelQueryAdapterImpl adapter, Query<T> query,
+                                                                        RawPatternMatcher rawPatternMatcher) {
+                super(adapter, query);
+                backend = rawPatternMatcher.getBackend();
+        }
+
+        @Override
+        protected void startListeningForChanges() {
+                backend.addUpdateListener(this, this, false);
+        }
+
+        @Override
+        protected void stopListeningForChanges() {
+                backend.removeUpdateListener(this);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalCursor.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalCursor.java
new file mode 100644
index 00000000..47efb2aa
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalCursor.java
@@ -0,0 +1,52 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.rete.index.IterableIndexer;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Iterator;
+
+class FunctionalCursor<T> implements Cursor<Tuple, T> {
+        private final IterableIndexer indexer;
+        private final Iterator<org.eclipse.viatra.query.runtime.matchers.tuple.Tuple> iterator;
+        private boolean terminated;
+        private Tuple key;
+        private T value;
+
+        public FunctionalCursor(IterableIndexer indexer) {
+                this.indexer = indexer;
+                iterator = indexer.getSignatures().iterator();
+        }
+
+        @Override
+        public Tuple getKey() {
+                return key;
+        }
+
+        @Override
+        public T getValue() {
+                return value;
+        }
+
+        @Override
+        public boolean isTerminated() {
+                return terminated;
+        }
+
+        @Override
+        public boolean move() {
+                if (!terminated && iterator.hasNext()) {
+                        var match = iterator.next();
+                        key = MatcherUtils.toRefineryTuple(match);
+                        value = MatcherUtils.getSingleValue(indexer.get(match));
+                        return true;
+                }
+                terminated = true;
+                return false;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalViatraMatcher.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalViatraMatcher.java
new file mode 100644
index 00000000..db4740cd
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/FunctionalViatraMatcher.java
@@ -0,0 +1,88 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import org.eclipse.viatra.query.runtime.rete.index.IterableIndexer;
+import org.eclipse.viatra.query.runtime.rete.matcher.RetePatternMatcher;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.query.dnf.FunctionalQuery;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
+import tools.refinery.store.tuple.Tuple;
+
+/**
+ * Directly access the tuples inside a VIATRA pattern matcher.<p>
+ * This class neglects calling
+ * {@link org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContext#wrapTuple(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple)}
+ * and
+ * {@link org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContext#unwrapTuple(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple)},
+ * because {@link tools.refinery.store.query.viatra.internal.context.RelationalRuntimeContext} provides a trivial
+ * implementation for these methods.
+ * Using this class with any other runtime context may lead to undefined behavior.
+ */
+public class FunctionalViatraMatcher<T> extends AbstractViatraMatcher<T> {
+        private final TupleMask emptyMask;
+        private final TupleMask omitOutputMask;
+        private final IterableIndexer omitOutputIndexer;
+
+        public FunctionalViatraMatcher(ViatraModelQueryAdapterImpl adapter, FunctionalQuery<T> query,
+                                                                   RawPatternMatcher rawPatternMatcher) {
+                super(adapter, query, rawPatternMatcher);
+                int arity = query.arity();
+                int arityWithOutput = arity + 1;
+                emptyMask = TupleMask.empty(arityWithOutput);
+                omitOutputMask = TupleMask.omit(arity, arityWithOutput);
+                if (backend instanceof RetePatternMatcher reteBackend) {
+                        var maybeIterableOmitOutputIndexer = IndexerUtils.getIndexer(reteBackend, omitOutputMask);
+                        if (maybeIterableOmitOutputIndexer instanceof IterableIndexer iterableOmitOutputIndexer) {
+                                omitOutputIndexer = iterableOmitOutputIndexer;
+                        } else {
+                                omitOutputIndexer = null;
+                        }
+                } else {
+                        omitOutputIndexer = null;
+                }
+        }
+
+        @Override
+        public T get(Tuple parameters) {
+                var tuple = MatcherUtils.toViatraTuple(parameters);
+                if (omitOutputIndexer == null) {
+                        return MatcherUtils.getSingleValue(backend.getAllMatches(omitOutputMask, tuple).iterator());
+                } else {
+                        return MatcherUtils.getSingleValue(omitOutputIndexer.get(tuple));
+                }
+        }
+
+        @Override
+        public Cursor<Tuple, T> getAll() {
+                if (omitOutputIndexer == null) {
+                        var allMatches = backend.getAllMatches(emptyMask, Tuples.staticArityFlatTupleOf());
+                        return new UnsafeFunctionalCursor<>(allMatches.iterator());
+                }
+                return new FunctionalCursor<>(omitOutputIndexer);
+        }
+
+        @Override
+        public int size() {
+                if (omitOutputIndexer == null) {
+                        return backend.countMatches(emptyMask, Tuples.staticArityFlatTupleOf());
+                }
+                return omitOutputIndexer.getBucketCount();
+        }
+
+        @Override
+        public void update(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple updateElement, boolean isInsertion) {
+                var key = MatcherUtils.keyToRefineryTuple(updateElement);
+                var value = MatcherUtils.<T>getValue(updateElement);
+                if (isInsertion) {
+                        notifyChange(key, null, value);
+                } else {
+                        notifyChange(key, value, null);
+                }
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/IndexerUtils.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/IndexerUtils.java
new file mode 100644
index 00000000..15f00b2d
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/IndexerUtils.java
@@ -0,0 +1,53 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.rete.index.Indexer;
+import org.eclipse.viatra.query.runtime.rete.matcher.ReteEngine;
+import org.eclipse.viatra.query.runtime.rete.matcher.RetePatternMatcher;
+import org.eclipse.viatra.query.runtime.rete.traceability.RecipeTraceInfo;
+
+import java.lang.invoke.MethodHandle;
+import java.lang.invoke.MethodHandles;
+import java.lang.invoke.MethodType;
+
+final class IndexerUtils {
+    private static final MethodHandle GET_ENGINE_HANDLE;
+    private static final MethodHandle GET_PRODUCTION_NODE_TRACE_HANDLE;
+    private static final MethodHandle ACCESS_PROJECTION_HANDLE;
+
+    static {
+        try {
+            var lookup = MethodHandles.privateLookupIn(RetePatternMatcher.class, MethodHandles.lookup());
+            GET_ENGINE_HANDLE = lookup.findGetter(RetePatternMatcher.class, "engine", ReteEngine.class);
+            GET_PRODUCTION_NODE_TRACE_HANDLE = lookup.findGetter(RetePatternMatcher.class, "productionNodeTrace",
+                    RecipeTraceInfo.class);
+            ACCESS_PROJECTION_HANDLE = lookup.findVirtual(ReteEngine.class, "accessProjection",
+                    MethodType.methodType(Indexer.class, RecipeTraceInfo.class, TupleMask.class));
+        } catch (IllegalAccessException | NoSuchFieldException | NoSuchMethodException e) {
+            throw new IllegalStateException("Cannot access private members of %s"
+                    .formatted(RetePatternMatcher.class.getPackageName()), e);
+        }
+    }
+
+    private IndexerUtils() {
+        throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+    }
+
+    public static Indexer getIndexer(RetePatternMatcher backend, TupleMask mask) {
+        try {
+            var engine = (ReteEngine) GET_ENGINE_HANDLE.invokeExact(backend);
+            var trace = (RecipeTraceInfo) GET_PRODUCTION_NODE_TRACE_HANDLE.invokeExact(backend);
+            return (Indexer) ACCESS_PROJECTION_HANDLE.invokeExact(engine, trace, mask);
+        } catch (Error e) {
+            // Fatal JVM errors should not be wrapped.
+            throw e;
+        } catch (Throwable e) {
+            throw new IllegalStateException("Cannot access matcher for mask " + mask, e);
+        }
+    }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtils.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtils.java
new file mode 100644
index 00000000..6e24812a
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtils.java
@@ -0,0 +1,115 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.tuple.*;
+
+import java.util.Iterator;
+
+final class MatcherUtils {
+        private MatcherUtils() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static org.eclipse.viatra.query.runtime.matchers.tuple.Tuple toViatraTuple(Tuple refineryTuple) {
+                if (refineryTuple instanceof Tuple0) {
+                        return Tuples.staticArityFlatTupleOf();
+                } else if (refineryTuple instanceof Tuple1) {
+                        return Tuples.staticArityFlatTupleOf(refineryTuple);
+                } else if (refineryTuple instanceof Tuple2 tuple2) {
+                        return Tuples.staticArityFlatTupleOf(Tuple.of(tuple2.value0()), Tuple.of(tuple2.value1()));
+                } else if (refineryTuple instanceof Tuple3 tuple3) {
+                        return Tuples.staticArityFlatTupleOf(Tuple.of(tuple3.value0()), Tuple.of(tuple3.value1()),
+                                        Tuple.of(tuple3.value2()));
+                } else if (refineryTuple instanceof Tuple4 tuple4) {
+                        return Tuples.staticArityFlatTupleOf(Tuple.of(tuple4.value0()), Tuple.of(tuple4.value1()),
+                                        Tuple.of(tuple4.value2()), Tuple.of(tuple4.value3()));
+                } else {
+                        int arity = refineryTuple.getSize();
+                        var values = new Object[arity];
+                        for (int i = 0; i < arity; i++) {
+                                values[i] = Tuple.of(refineryTuple.get(i));
+                        }
+                        return Tuples.flatTupleOf(values);
+                }
+        }
+
+        public static Tuple toRefineryTuple(ITuple viatraTuple) {
+                int arity = viatraTuple.getSize();
+                if (arity == 1) {
+                        return getWrapper(viatraTuple, 0);
+                }
+                return prefixToRefineryTuple(viatraTuple, viatraTuple.getSize());
+        }
+
+        public static Tuple keyToRefineryTuple(ITuple viatraTuple) {
+                return prefixToRefineryTuple(viatraTuple, viatraTuple.getSize() - 1);
+        }
+
+        private static Tuple prefixToRefineryTuple(ITuple viatraTuple, int targetArity) {
+                if (targetArity < 0) {
+                        throw new IllegalArgumentException("Requested negative prefix %d of %s"
+                                        .formatted(targetArity, viatraTuple));
+                }
+                return switch (targetArity) {
+                        case 0 -> Tuple.of();
+                        case 1 -> Tuple.of(unwrap(viatraTuple, 0));
+                        case 2 -> Tuple.of(unwrap(viatraTuple, 0), unwrap(viatraTuple, 1));
+                        case 3 -> Tuple.of(unwrap(viatraTuple, 0), unwrap(viatraTuple, 1), unwrap(viatraTuple, 2));
+                        case 4 -> Tuple.of(unwrap(viatraTuple, 0), unwrap(viatraTuple, 1), unwrap(viatraTuple, 2),
+                                        unwrap(viatraTuple, 3));
+                        default -> {
+                                var entries = new int[targetArity];
+                                for (int i = 0; i < targetArity; i++) {
+                                        entries[i] = unwrap(viatraTuple, i);
+                                }
+                                yield Tuple.of(entries);
+                        }
+                };
+        }
+
+        private static Tuple1 getWrapper(ITuple viatraTuple, int index) {
+                if (!((viatraTuple.get(index)) instanceof Tuple1 wrappedObjectId)) {
+                        throw new IllegalArgumentException("Element %d of tuple %s is not an object id"
+                                        .formatted(index, viatraTuple));
+                }
+                return wrappedObjectId;
+        }
+
+        private static int unwrap(ITuple viatraTuple, int index) {
+                return getWrapper(viatraTuple, index).value0();
+        }
+
+        public static <T> T getValue(ITuple match) {
+                // This is only safe if we know for sure that match came from a functional query of type {@code T}.
+                @SuppressWarnings("unchecked")
+                var result = (T) match.get(match.getSize() - 1);
+                return result;
+        }
+
+        public static <T> T getSingleValue(@Nullable Iterable<? extends ITuple> viatraTuples) {
+                if (viatraTuples == null) {
+                        return null;
+                }
+                return getSingleValue(viatraTuples.iterator());
+        }
+
+        public static <T> T getSingleValue(Iterator<? extends ITuple> iterator) {
+                if (!iterator.hasNext()) {
+                        return null;
+                }
+                var match = iterator.next();
+                var result = MatcherUtils.<T>getValue(match);
+                if (iterator.hasNext()) {
+                        var input = keyToRefineryTuple(match);
+                        throw new IllegalStateException("Query is not functional for input tuple: " + input);
+                }
+                return result;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RawPatternMatcher.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RawPatternMatcher.java
new file mode 100644
index 00000000..5b82c4b7
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RawPatternMatcher.java
@@ -0,0 +1,20 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.api.GenericPatternMatcher;
+import org.eclipse.viatra.query.runtime.api.GenericQuerySpecification;
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryResultProvider;
+
+public class RawPatternMatcher extends GenericPatternMatcher {
+    public RawPatternMatcher(GenericQuerySpecification<? extends GenericPatternMatcher> specification) {
+        super(specification);
+    }
+
+        IQueryResultProvider getBackend() {
+                return backend;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalCursor.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalCursor.java
new file mode 100644
index 00000000..1dc8f5db
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalCursor.java
@@ -0,0 +1,47 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Iterator;
+
+class RelationalCursor implements Cursor<Tuple, Boolean> {
+    private final Iterator<? extends ITuple> tuplesIterator;
+    private boolean terminated;
+    private Tuple key;
+
+    public RelationalCursor(Iterator<? extends ITuple> tuplesIterator) {
+        this.tuplesIterator = tuplesIterator;
+    }
+
+    @Override
+    public Tuple getKey() {
+        return key;
+    }
+
+    @Override
+    public Boolean getValue() {
+        return true;
+    }
+
+    @Override
+    public boolean isTerminated() {
+        return terminated;
+    }
+
+    @Override
+    public boolean move() {
+        if (!terminated && tuplesIterator.hasNext()) {
+            key = MatcherUtils.toRefineryTuple(tuplesIterator.next());
+            return true;
+        }
+        terminated = true;
+        return false;
+    }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalViatraMatcher.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalViatraMatcher.java
new file mode 100644
index 00000000..ac95dcc0
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/RelationalViatraMatcher.java
@@ -0,0 +1,80 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.TupleMask;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import org.eclipse.viatra.query.runtime.rete.index.Indexer;
+import org.eclipse.viatra.query.runtime.rete.matcher.RetePatternMatcher;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.map.Cursors;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
+import tools.refinery.store.tuple.Tuple;
+
+/**
+ * Directly access the tuples inside a VIATRA pattern matcher.<p>
+ * This class neglects calling
+ * {@link org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContext#wrapTuple(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple)}
+ * and
+ * {@link org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContext#unwrapTuple(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple)},
+ * because {@link tools.refinery.store.query.viatra.internal.context.RelationalRuntimeContext} provides a trivial
+ * implementation for these methods.
+ * Using this class with any other runtime context may lead to undefined behavior.
+ */
+public class RelationalViatraMatcher extends AbstractViatraMatcher<Boolean> {
+        private final TupleMask emptyMask;
+        private final TupleMask identityMask;
+        private final Indexer emptyMaskIndexer;
+
+        public RelationalViatraMatcher(ViatraModelQueryAdapterImpl adapter, RelationalQuery query,
+                                                                   RawPatternMatcher rawPatternMatcher) {
+                super(adapter, query, rawPatternMatcher);
+                int arity = query.arity();
+                emptyMask = TupleMask.empty(arity);
+                identityMask = TupleMask.identity(arity);
+                if (backend instanceof RetePatternMatcher reteBackend) {
+                        emptyMaskIndexer = IndexerUtils.getIndexer(reteBackend, emptyMask);
+                } else {
+                        emptyMaskIndexer = null;
+                }
+        }
+
+        @Override
+        public Boolean get(Tuple parameters) {
+                var tuple = MatcherUtils.toViatraTuple(parameters);
+                if (emptyMaskIndexer == null) {
+                        return backend.hasMatch(identityMask, tuple);
+                }
+                var matches = emptyMaskIndexer.get(Tuples.staticArityFlatTupleOf());
+                return matches != null && matches.contains(tuple);
+        }
+
+        @Override
+        public Cursor<Tuple, Boolean> getAll() {
+                if (emptyMaskIndexer == null) {
+                        var allMatches = backend.getAllMatches(emptyMask, Tuples.staticArityFlatTupleOf());
+                        return new RelationalCursor(allMatches.iterator());
+                }
+                var matches = emptyMaskIndexer.get(Tuples.staticArityFlatTupleOf());
+                return matches == null ? Cursors.empty() : new RelationalCursor(matches.stream().iterator());
+        }
+
+        @Override
+        public int size() {
+                if (emptyMaskIndexer == null) {
+                        return backend.countMatches(emptyMask, Tuples.staticArityFlatTupleOf());
+                }
+                var matches = emptyMaskIndexer.get(Tuples.staticArityFlatTupleOf());
+                return matches == null ? 0 : matches.size();
+        }
+
+        @Override
+        public void update(org.eclipse.viatra.query.runtime.matchers.tuple.Tuple updateElement, boolean isInsertion) {
+                var key = MatcherUtils.toRefineryTuple(updateElement);
+                notifyChange(key, !isInsertion, isInsertion);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/UnsafeFunctionalCursor.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/UnsafeFunctionalCursor.java
new file mode 100644
index 00000000..b0b507fe
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/matcher/UnsafeFunctionalCursor.java
@@ -0,0 +1,55 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Iterator;
+
+/**
+ * Cursor for a functional result set that iterates over a stream of raw matches and doesn't check whether the
+ * functional dependency of the output on the inputs is obeyed.
+ * @param <T> The output type.
+ */
+class UnsafeFunctionalCursor<T> implements Cursor<Tuple, T> {
+        private final Iterator<? extends ITuple> tuplesIterator;
+        private boolean terminated;
+        private Tuple key;
+        private T value;
+
+        public UnsafeFunctionalCursor(Iterator<? extends ITuple> tuplesIterator) {
+                this.tuplesIterator = tuplesIterator;
+        }
+
+        @Override
+        public Tuple getKey() {
+                return key;
+        }
+
+        @Override
+        public T getValue() {
+                return value;
+        }
+
+        @Override
+        public boolean isTerminated() {
+                return terminated;
+        }
+
+        @Override
+        public boolean move() {
+                if (!terminated && tuplesIterator.hasNext()) {
+                        var match = tuplesIterator.next();
+                        key = MatcherUtils.keyToRefineryTuple(match);
+                        value = MatcherUtils.getValue(match);
+                        return true;
+                }
+                terminated = true;
+                return false;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/AssumptionEvaluator.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/AssumptionEvaluator.java
new file mode 100644
index 00000000..cf127291
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/AssumptionEvaluator.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.psystem.IValueProvider;
+import tools.refinery.store.query.term.Term;
+
+class AssumptionEvaluator extends TermEvaluator<Boolean> {
+        public AssumptionEvaluator(Term<Boolean> term) {
+                super(term);
+        }
+
+        @Override
+        public Object evaluateExpression(IValueProvider provider) {
+                var result = super.evaluateExpression(provider);
+                return result == null ? Boolean.FALSE : result;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/DNF2PQuery.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/DNF2PQuery.java
deleted file mode 100644
index 60f1bcae..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/DNF2PQuery.java
+++ /dev/null
@@ -1,223 +0,0 @@
-package tools.refinery.store.query.viatra.internal.pquery;
-
-import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
-import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
-import org.eclipse.viatra.query.runtime.matchers.psystem.PBody;
-import org.eclipse.viatra.query.runtime.matchers.psystem.PVariable;
-import org.eclipse.viatra.query.runtime.matchers.psystem.annotations.PAnnotation;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.Equality;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.ExportedParameter;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.Inequality;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.NegativePatternCall;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.BinaryTransitiveClosure;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.ConstantValue;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.PositivePatternCall;
-import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.TypeConstraint;
-import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PParameter;
-import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PVisibility;
-import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
-import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.DNFAnd;
-import tools.refinery.store.query.DNFUtils;
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.atom.*;
-import tools.refinery.store.query.view.AnyRelationView;
-
-import java.util.*;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
-public class DNF2PQuery {
-        private static final Object P_CONSTRAINT_LOCK = new Object();
-
-        private final Set<DNF> translating = new LinkedHashSet<>();
-
-        private final Map<DNF, RawPQuery> dnf2PQueryMap = new HashMap<>();
-
-        private final Map<AnyRelationView, RelationViewWrapper> view2WrapperMap = new LinkedHashMap<>();
-
-        private final Map<AnyRelationView, RawPQuery> view2EmbeddedMap = new HashMap<>();
-
-        private Function<DNF, QueryEvaluationHint> computeHint = dnf -> new QueryEvaluationHint(null,
-                        QueryEvaluationHint.BackendRequirement.UNSPECIFIED);
-
-        public void setComputeHint(Function<DNF, QueryEvaluationHint> computeHint) {
-                this.computeHint = computeHint;
-        }
-
-        public RawPQuery translate(DNF dnfQuery) {
-                if (translating.contains(dnfQuery)) {
-                        var path = translating.stream().map(DNF::name).collect(Collectors.joining(" -> "));
-                        throw new IllegalStateException("Circular reference %s -> %s detected".formatted(path,
-                                        dnfQuery.name()));
-                }
-                // We can't use computeIfAbsent here, because translating referenced queries calls this method in a reentrant
-                // way, which would cause a ConcurrentModificationException with computeIfAbsent.
-                var pQuery = dnf2PQueryMap.get(dnfQuery);
-                if (pQuery == null) {
-                        translating.add(dnfQuery);
-                        try {
-                                pQuery = doTranslate(dnfQuery);
-                                dnf2PQueryMap.put(dnfQuery, pQuery);
-                        } finally {
-                                translating.remove(dnfQuery);
-                        }
-                }
-                return pQuery;
-        }
-
-        public Map<AnyRelationView, IInputKey> getRelationViews() {
-                return Collections.unmodifiableMap(view2WrapperMap);
-        }
-
-        public RawPQuery getAlreadyTranslated(DNF dnfQuery) {
-                return dnf2PQueryMap.get(dnfQuery);
-        }
-
-        private RawPQuery doTranslate(DNF dnfQuery) {
-                var pQuery = new RawPQuery(dnfQuery.getUniqueName());
-                pQuery.setEvaluationHints(computeHint.apply(dnfQuery));
-
-                Map<Variable, PParameter> parameters = new HashMap<>();
-                for (Variable variable : dnfQuery.getParameters()) {
-                        parameters.put(variable, new PParameter(variable.getUniqueName()));
-                }
-
-                List<PParameter> parameterList = new ArrayList<>();
-                for (var param : dnfQuery.getParameters()) {
-                        parameterList.add(parameters.get(param));
-                }
-                pQuery.setParameters(parameterList);
-
-                for (var functionalDependency : dnfQuery.getFunctionalDependencies()) {
-                        var functionalDependencyAnnotation = new PAnnotation("FunctionalDependency");
-                        for (var forEachVariable : functionalDependency.forEach()) {
-                                functionalDependencyAnnotation.addAttribute("forEach", forEachVariable.getUniqueName());
-                        }
-                        for (var uniqueVariable : functionalDependency.unique()) {
-                                functionalDependencyAnnotation.addAttribute("unique", uniqueVariable.getUniqueName());
-                        }
-                        pQuery.addAnnotation(functionalDependencyAnnotation);
-                }
-
-                // The constructor of {@link org.eclipse.viatra.query.runtime.matchers.psystem.BasePConstraint} mutates
-                // global static state (<code>nextID</code>) without locking. Therefore, we need to synchronize before creating
-                // any query constraints to avoid a data race.
-                synchronized (P_CONSTRAINT_LOCK) {
-                        for (DNFAnd clause : dnfQuery.getClauses()) {
-                                PBody body = new PBody(pQuery);
-                                List<ExportedParameter> symbolicParameters = new ArrayList<>();
-                                for (var param : dnfQuery.getParameters()) {
-                                        PVariable pVar = body.getOrCreateVariableByName(param.getUniqueName());
-                                        symbolicParameters.add(new ExportedParameter(body, pVar, parameters.get(param)));
-                                }
-                                body.setSymbolicParameters(symbolicParameters);
-                                pQuery.addBody(body);
-                                for (DNFAtom constraint : clause.constraints()) {
-                                        translateDNFAtom(constraint, body);
-                                }
-                        }
-                }
-
-                return pQuery;
-        }
-
-        private void translateDNFAtom(DNFAtom constraint, PBody body) {
-                if (constraint instanceof EquivalenceAtom equivalenceAtom) {
-                        translateEquivalenceAtom(equivalenceAtom, body);
-                } else if (constraint instanceof RelationViewAtom relationViewAtom) {
-                        translateRelationViewAtom(relationViewAtom, body);
-                } else if (constraint instanceof DNFCallAtom callAtom) {
-                        translateCallAtom(callAtom, body);
-                } else if (constraint instanceof ConstantAtom constantAtom) {
-                        translateConstantAtom(constantAtom, body);
-                } else {
-                        throw new IllegalArgumentException("Unknown constraint: " + constraint.toString());
-                }
-        }
-
-        private void translateEquivalenceAtom(EquivalenceAtom equivalence, PBody body) {
-                PVariable varSource = body.getOrCreateVariableByName(equivalence.left().getUniqueName());
-                PVariable varTarget = body.getOrCreateVariableByName(equivalence.right().getUniqueName());
-                if (equivalence.positive()) {
-                        new Equality(body, varSource, varTarget);
-                } else {
-                        new Inequality(body, varSource, varTarget);
-                }
-        }
-
-        private void translateRelationViewAtom(RelationViewAtom relationViewAtom, PBody body) {
-                var substitution = translateSubstitution(relationViewAtom.getSubstitution(), body);
-                var polarity = relationViewAtom.getPolarity();
-                var relationView = relationViewAtom.getTarget();
-                if (polarity == CallPolarity.POSITIVE) {
-                        new TypeConstraint(body, substitution, wrapView(relationView));
-                } else {
-                        var embeddedPQuery = translateEmbeddedRelationViewPQuery(relationView);
-                        switch (polarity) {
-                        case TRANSITIVE -> new BinaryTransitiveClosure(body, substitution, embeddedPQuery);
-                        case NEGATIVE -> new NegativePatternCall(body, substitution, embeddedPQuery);
-                        default -> throw new IllegalArgumentException("Unknown polarity: " + polarity);
-                        }
-                }
-        }
-
-        private static Tuple translateSubstitution(List<Variable> substitution, PBody body) {
-                int arity = substitution.size();
-                Object[] variables = new Object[arity];
-                for (int i = 0; i < arity; i++) {
-                        var variable = substitution.get(i);
-                        variables[i] = body.getOrCreateVariableByName(variable.getUniqueName());
-                }
-                return Tuples.flatTupleOf(variables);
-        }
-
-        private RawPQuery translateEmbeddedRelationViewPQuery(AnyRelationView relationView) {
-                return view2EmbeddedMap.computeIfAbsent(relationView, this::doTranslateEmbeddedRelationViewPQuery);
-        }
-
-        private RawPQuery doTranslateEmbeddedRelationViewPQuery(AnyRelationView relationView) {
-                var embeddedPQuery = new RawPQuery(DNFUtils.generateUniqueName(relationView.name()), PVisibility.EMBEDDED);
-                var body = new PBody(embeddedPQuery);
-                int arity = relationView.arity();
-                var parameters = new ArrayList<PParameter>(arity);
-                var arguments = new Object[arity];
-                var symbolicParameters = new ArrayList<ExportedParameter>(arity);
-                for (int i = 0; i < arity; i++) {
-                        var parameterName = "p" + i;
-                        var parameter = new PParameter(parameterName);
-                        parameters.add(parameter);
-                        var variable = body.getOrCreateVariableByName(parameterName);
-                        arguments[i] = variable;
-                        symbolicParameters.add(new ExportedParameter(body, variable, parameter));
-                }
-                embeddedPQuery.setParameters(parameters);
-                body.setSymbolicParameters(symbolicParameters);
-                var argumentTuple = Tuples.flatTupleOf(arguments);
-                new TypeConstraint(body, argumentTuple, wrapView(relationView));
-                embeddedPQuery.addBody(body);
-                return embeddedPQuery;
-        }
-
-        private RelationViewWrapper wrapView(AnyRelationView relationView) {
-                return view2WrapperMap.computeIfAbsent(relationView, RelationViewWrapper::new);
-        }
-
-        private void translateCallAtom(DNFCallAtom callAtom, PBody body) {
-                var variablesTuple = translateSubstitution(callAtom.getSubstitution(), body);
-                var translatedReferred = translate(callAtom.getTarget());
-                var polarity = callAtom.getPolarity();
-                switch (polarity) {
-                case POSITIVE -> new PositivePatternCall(body, variablesTuple, translatedReferred);
-                case TRANSITIVE -> new BinaryTransitiveClosure(body, variablesTuple, translatedReferred);
-                case NEGATIVE -> new NegativePatternCall(body, variablesTuple, translatedReferred);
-                default -> throw new IllegalArgumentException("Unknown polarity: " + polarity);
-                }
-        }
-
-        private void translateConstantAtom(ConstantAtom constantAtom, PBody body) {
-                var variable = body.getOrCreateVariableByName(constantAtom.variable().getUniqueName());
-                new ConstantValue(body, variable, constantAtom.nodeId());
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/Dnf2PQuery.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/Dnf2PQuery.java
new file mode 100644
index 00000000..5b0ea61d
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/Dnf2PQuery.java
@@ -0,0 +1,266 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.IQueryBackendFactory;
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.psystem.PBody;
+import org.eclipse.viatra.query.runtime.matchers.psystem.PVariable;
+import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.BoundAggregator;
+import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.IMultisetAggregationOperator;
+import org.eclipse.viatra.query.runtime.matchers.psystem.annotations.PAnnotation;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.*;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.BinaryTransitiveClosure;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.ConstantValue;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.PositivePatternCall;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.TypeConstraint;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PParameter;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PParameterDirection;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PQuery;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.DnfClause;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.literal.*;
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.StatefulAggregator;
+import tools.refinery.store.query.term.StatelessAggregator;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.util.CycleDetectingMapper;
+
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+public class Dnf2PQuery {
+        private static final Object P_CONSTRAINT_LOCK = new Object();
+        private final CycleDetectingMapper<Dnf, RawPQuery> mapper = new CycleDetectingMapper<>(Dnf::name,
+                        this::doTranslate);
+        private final QueryWrapperFactory wrapperFactory = new QueryWrapperFactory(this);
+        private final Map<Dnf, QueryEvaluationHint> hintOverrides = new LinkedHashMap<>();
+        private Function<Dnf, QueryEvaluationHint> computeHint = dnf -> new QueryEvaluationHint(null,
+                        (IQueryBackendFactory) null);
+
+        public void setComputeHint(Function<Dnf, QueryEvaluationHint> computeHint) {
+                this.computeHint = computeHint;
+        }
+
+        public RawPQuery translate(Dnf dnfQuery) {
+                return mapper.map(dnfQuery);
+        }
+
+        public Map<AnySymbolView, IInputKey> getSymbolViews() {
+                return wrapperFactory.getSymbolViews();
+        }
+
+        public void hint(Dnf dnf, QueryEvaluationHint hint) {
+                hintOverrides.compute(dnf, (ignoredKey, existingHint) ->
+                                existingHint == null ? hint : existingHint.overrideBy(hint));
+        }
+
+        private QueryEvaluationHint consumeHint(Dnf dnf) {
+                var defaultHint = computeHint.apply(dnf);
+                var existingHint = hintOverrides.remove(dnf);
+                return defaultHint.overrideBy(existingHint);
+        }
+
+        public void assertNoUnusedHints() {
+                if (hintOverrides.isEmpty()) {
+                        return;
+                }
+                var unusedHints = hintOverrides.keySet().stream().map(Dnf::name).collect(Collectors.joining(", "));
+                throw new IllegalStateException(
+                                "Unused query evaluation hints for %s. Hints must be set before a query is added to the engine"
+                                                .formatted(unusedHints));
+        }
+
+        private RawPQuery doTranslate(Dnf dnfQuery) {
+                var pQuery = new RawPQuery(dnfQuery.getUniqueName());
+                pQuery.setEvaluationHints(consumeHint(dnfQuery));
+
+                Map<SymbolicParameter, PParameter> parameters = new HashMap<>();
+                List<PParameter> parameterList = new ArrayList<>();
+                for (var parameter : dnfQuery.getSymbolicParameters()) {
+                        var direction = switch (parameter.getDirection()) {
+                                case OUT -> parameter.isUnifiable() ? PParameterDirection.INOUT : PParameterDirection.OUT;
+                                case IN -> throw new IllegalArgumentException("Query %s with input parameter %s is not supported"
+                                                .formatted(dnfQuery, parameter.getVariable()));
+                        };
+                        var pParameter = new PParameter(parameter.getVariable().getUniqueName(), null, null, direction);
+                        parameters.put(parameter, pParameter);
+                        parameterList.add(pParameter);
+                }
+
+                pQuery.setParameters(parameterList);
+
+                for (var functionalDependency : dnfQuery.getFunctionalDependencies()) {
+                        var functionalDependencyAnnotation = new PAnnotation("FunctionalDependency");
+                        for (var forEachVariable : functionalDependency.forEach()) {
+                                functionalDependencyAnnotation.addAttribute("forEach", forEachVariable.getUniqueName());
+                        }
+                        for (var uniqueVariable : functionalDependency.unique()) {
+                                functionalDependencyAnnotation.addAttribute("unique", uniqueVariable.getUniqueName());
+                        }
+                        pQuery.addAnnotation(functionalDependencyAnnotation);
+                }
+
+                // The constructor of {@link org.eclipse.viatra.query.runtime.matchers.psystem.BasePConstraint} mutates
+                // global static state (<code>nextID</code>) without locking. Therefore, we need to synchronize before creating
+                // any query literals to avoid a data race.
+                synchronized (P_CONSTRAINT_LOCK) {
+                        for (DnfClause clause : dnfQuery.getClauses()) {
+                                PBody body = new PBody(pQuery);
+                                List<ExportedParameter> parameterExports = new ArrayList<>();
+                                for (var parameter : dnfQuery.getSymbolicParameters()) {
+                                        PVariable pVar = body.getOrCreateVariableByName(parameter.getVariable().getUniqueName());
+                                        parameterExports.add(new ExportedParameter(body, pVar, parameters.get(parameter)));
+                                }
+                                body.setSymbolicParameters(parameterExports);
+                                pQuery.addBody(body);
+                                for (Literal literal : clause.literals()) {
+                                        translateLiteral(literal, body);
+                                }
+                        }
+                }
+
+                return pQuery;
+        }
+
+        private void translateLiteral(Literal literal, PBody body) {
+                if (literal instanceof EquivalenceLiteral equivalenceLiteral) {
+                        translateEquivalenceLiteral(equivalenceLiteral, body);
+                } else if (literal instanceof CallLiteral callLiteral) {
+                        translateCallLiteral(callLiteral, body);
+                } else if (literal instanceof ConstantLiteral constantLiteral) {
+                        translateConstantLiteral(constantLiteral, body);
+                } else if (literal instanceof AssignLiteral<?> assignLiteral) {
+                        translateAssignLiteral(assignLiteral, body);
+                } else if (literal instanceof AssumeLiteral assumeLiteral) {
+                        translateAssumeLiteral(assumeLiteral, body);
+                } else if (literal instanceof CountLiteral countLiteral) {
+                        translateCountLiteral(countLiteral, body);
+                } else if (literal instanceof AggregationLiteral<?, ?> aggregationLiteral) {
+                        translateAggregationLiteral(aggregationLiteral, body);
+                } else {
+                        throw new IllegalArgumentException("Unknown literal: " + literal.toString());
+                }
+        }
+
+        private void translateEquivalenceLiteral(EquivalenceLiteral equivalenceLiteral, PBody body) {
+                PVariable varSource = body.getOrCreateVariableByName(equivalenceLiteral.left().getUniqueName());
+                PVariable varTarget = body.getOrCreateVariableByName(equivalenceLiteral.right().getUniqueName());
+                if (equivalenceLiteral.positive()) {
+                        new Equality(body, varSource, varTarget);
+                } else {
+                        new Inequality(body, varSource, varTarget);
+                }
+        }
+
+        private void translateCallLiteral(CallLiteral callLiteral, PBody body) {
+                var polarity = callLiteral.getPolarity();
+                switch (polarity) {
+                case POSITIVE -> {
+                        var substitution = translateSubstitution(callLiteral.getArguments(), body);
+                        var constraint = callLiteral.getTarget();
+                        if (constraint instanceof Dnf dnf) {
+                                var pattern = translate(dnf);
+                                new PositivePatternCall(body, substitution, pattern);
+                        } else if (constraint instanceof AnySymbolView symbolView) {
+                                var inputKey = wrapperFactory.getInputKey(symbolView);
+                                new TypeConstraint(body, substitution, inputKey);
+                        } else {
+                                throw new IllegalArgumentException("Unknown Constraint: " + constraint);
+                        }
+                }
+                case TRANSITIVE -> {
+                        var substitution = translateSubstitution(callLiteral.getArguments(), body);
+                        var constraint = callLiteral.getTarget();
+                        PQuery pattern;
+                        if (constraint instanceof Dnf dnf) {
+                                pattern = translate(dnf);
+                        } else if (constraint instanceof AnySymbolView symbolView) {
+                                pattern = wrapperFactory.wrapSymbolViewIdentityArguments(symbolView);
+                        } else {
+                                throw new IllegalArgumentException("Unknown Constraint: " + constraint);
+                        }
+                        new BinaryTransitiveClosure(body, substitution, pattern);
+                }
+                case NEGATIVE -> {
+                        var wrappedCall = wrapperFactory.maybeWrapConstraint(callLiteral);
+                        var substitution = translateSubstitution(wrappedCall.remappedArguments(), body);
+                        var pattern = wrappedCall.pattern();
+                        new NegativePatternCall(body, substitution, pattern);
+                }
+                default -> throw new IllegalArgumentException("Unknown polarity: " + polarity);
+                }
+        }
+
+        private static Tuple translateSubstitution(List<Variable> substitution, PBody body) {
+                int arity = substitution.size();
+                Object[] variables = new Object[arity];
+                for (int i = 0; i < arity; i++) {
+                        var variable = substitution.get(i);
+                        variables[i] = body.getOrCreateVariableByName(variable.getUniqueName());
+                }
+                return Tuples.flatTupleOf(variables);
+        }
+
+        private void translateConstantLiteral(ConstantLiteral constantLiteral, PBody body) {
+                var variable = body.getOrCreateVariableByName(constantLiteral.variable().getUniqueName());
+                new ConstantValue(body, variable, constantLiteral.nodeId());
+        }
+
+        private <T> void translateAssignLiteral(AssignLiteral<T> assignLiteral, PBody body) {
+                var variable = body.getOrCreateVariableByName(assignLiteral.variable().getUniqueName());
+                var term = assignLiteral.term();
+                if (term instanceof ConstantTerm<T> constantTerm) {
+                        new ConstantValue(body, variable, constantTerm.getValue());
+                } else {
+                        var evaluator = new TermEvaluator<>(term);
+                        new ExpressionEvaluation(body, evaluator, variable);
+                }
+        }
+
+        private void translateAssumeLiteral(AssumeLiteral assumeLiteral, PBody body) {
+                var evaluator = new AssumptionEvaluator(assumeLiteral.term());
+                new ExpressionEvaluation(body, evaluator, null);
+        }
+
+        private void translateCountLiteral(CountLiteral countLiteral, PBody body) {
+                var wrappedCall = wrapperFactory.maybeWrapConstraint(countLiteral);
+                var substitution = translateSubstitution(wrappedCall.remappedArguments(), body);
+                var resultVariable = body.getOrCreateVariableByName(countLiteral.getResultVariable().getUniqueName());
+                new PatternMatchCounter(body, substitution, wrappedCall.pattern(), resultVariable);
+        }
+
+        private <R, T> void translateAggregationLiteral(AggregationLiteral<R, T> aggregationLiteral, PBody body) {
+                var aggregator = aggregationLiteral.getAggregator();
+                IMultisetAggregationOperator<T, ?, R> aggregationOperator;
+                if (aggregator instanceof StatelessAggregator<R, T> statelessAggregator) {
+                        aggregationOperator = new StatelessMultisetAggregator<>(statelessAggregator);
+                } else if (aggregator instanceof StatefulAggregator<R, T> statefulAggregator) {
+                        aggregationOperator = new StatefulMultisetAggregator<>(statefulAggregator);
+                } else {
+                        throw new IllegalArgumentException("Unknown aggregator: " + aggregator);
+                }
+                var wrappedCall = wrapperFactory.maybeWrapConstraint(aggregationLiteral);
+                var substitution = translateSubstitution(wrappedCall.remappedArguments(), body);
+                var inputVariable = body.getOrCreateVariableByName(aggregationLiteral.getInputVariable().getUniqueName());
+                var aggregatedColumn = substitution.invertIndex().get(inputVariable);
+                if (aggregatedColumn == null) {
+                        throw new IllegalStateException("Input variable %s not found in substitution %s".formatted(inputVariable,
+                                        substitution));
+                }
+                var boundAggregator = new BoundAggregator(aggregationOperator, aggregator.getInputType(),
+                                aggregator.getResultType());
+                var resultVariable = body.getOrCreateVariableByName(aggregationLiteral.getResultVariable().getUniqueName());
+                new AggregatorConstraint(boundAggregator, body, substitution, wrappedCall.pattern(), resultVariable,
+                                aggregatedColumn);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/QueryWrapperFactory.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/QueryWrapperFactory.java
new file mode 100644
index 00000000..2b7280f2
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/QueryWrapperFactory.java
@@ -0,0 +1,189 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.psystem.PBody;
+import org.eclipse.viatra.query.runtime.matchers.psystem.PVariable;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicdeferred.ExportedParameter;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.PositivePatternCall;
+import org.eclipse.viatra.query.runtime.matchers.psystem.basicenumerables.TypeConstraint;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PParameter;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PQuery;
+import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PVisibility;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.DnfUtils;
+import tools.refinery.store.query.literal.AbstractCallLiteral;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.SymbolView;
+import tools.refinery.store.util.CycleDetectingMapper;
+
+import java.util.*;
+import java.util.function.ToIntFunction;
+
+class QueryWrapperFactory {
+        private final Dnf2PQuery dnf2PQuery;
+        private final Map<AnySymbolView, SymbolViewWrapper> view2WrapperMap = new LinkedHashMap<>();
+        private final CycleDetectingMapper<RemappedConstraint, RawPQuery> wrapConstraint = new CycleDetectingMapper<>(
+                        RemappedConstraint::toString, this::doWrapConstraint);
+
+        QueryWrapperFactory(Dnf2PQuery dnf2PQuery) {
+                this.dnf2PQuery = dnf2PQuery;
+        }
+
+        public PQuery wrapSymbolViewIdentityArguments(AnySymbolView symbolView) {
+                var identity = new int[symbolView.arity()];
+                for (int i = 0; i < identity.length; i++) {
+                        identity[i] = i;
+                }
+                return maybeWrapConstraint(symbolView, identity);
+        }
+
+        public WrappedCall maybeWrapConstraint(AbstractCallLiteral callLiteral) {
+                var arguments = callLiteral.getArguments();
+                int arity = arguments.size();
+                var remappedParameters = new int[arity];
+                var unboundVariableIndices = new HashMap<Variable, Integer>();
+                var appendVariable = new VariableAppender();
+                for (int i = 0; i < arity; i++) {
+                        var variable = arguments.get(i);
+                        // Unify all variables to avoid VIATRA bugs, even if they're bound in the containing clause.
+                        remappedParameters[i] = unboundVariableIndices.computeIfAbsent(variable, appendVariable::applyAsInt);
+                }
+                var pattern = maybeWrapConstraint(callLiteral.getTarget(), remappedParameters);
+                return new WrappedCall(pattern, appendVariable.getRemappedArguments());
+        }
+
+        private PQuery maybeWrapConstraint(Constraint constraint, int[] remappedParameters) {
+                if (remappedParameters.length != constraint.arity()) {
+                        throw new IllegalArgumentException("Constraint %s expected %d parameters, but got %d parameters".formatted(
+                                        constraint, constraint.arity(), remappedParameters.length));
+                }
+                if (constraint instanceof Dnf dnf && isIdentity(remappedParameters)) {
+                        return dnf2PQuery.translate(dnf);
+                }
+                return wrapConstraint.map(new RemappedConstraint(constraint, remappedParameters));
+        }
+
+        private static boolean isIdentity(int[] remappedParameters) {
+                for (int i = 0; i < remappedParameters.length; i++) {
+                        if (remappedParameters[i] != i) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+
+        private RawPQuery doWrapConstraint(RemappedConstraint remappedConstraint) {
+                var constraint = remappedConstraint.constraint();
+                var remappedParameters = remappedConstraint.remappedParameters();
+
+                checkNoInputParameters(constraint);
+
+                var embeddedPQuery = new RawPQuery(DnfUtils.generateUniqueName(constraint.name()), PVisibility.EMBEDDED);
+                var body = new PBody(embeddedPQuery);
+                int arity = Arrays.stream(remappedParameters).max().orElse(-1) + 1;
+                var parameters = new ArrayList<PParameter>(arity);
+                var parameterVariables = new PVariable[arity];
+                var symbolicParameters = new ArrayList<ExportedParameter>(arity);
+                for (int i = 0; i < arity; i++) {
+                        var parameterName = "p" + i;
+                        var parameter = new PParameter(parameterName);
+                        parameters.add(parameter);
+                        var variable = body.getOrCreateVariableByName(parameterName);
+                        parameterVariables[i] = variable;
+                        symbolicParameters.add(new ExportedParameter(body, variable, parameter));
+                }
+                embeddedPQuery.setParameters(parameters);
+                body.setSymbolicParameters(symbolicParameters);
+
+                var arguments = new Object[remappedParameters.length];
+                for (int i = 0; i < remappedParameters.length; i++) {
+                        arguments[i] = parameterVariables[remappedParameters[i]];
+                }
+                var argumentTuple = Tuples.flatTupleOf(arguments);
+
+                addPositiveConstraint(constraint, body, argumentTuple);
+                embeddedPQuery.addBody(body);
+                return embeddedPQuery;
+        }
+
+        private static void checkNoInputParameters(Constraint constraint) {
+                for (var constraintParameter : constraint.getParameters()) {
+                        if (constraintParameter.getDirection() == ParameterDirection.IN) {
+                                throw new IllegalArgumentException("Input parameter %s of %s is not supported"
+                                                .formatted(constraintParameter, constraint));
+                        }
+                }
+        }
+
+        private void addPositiveConstraint(Constraint constraint, PBody body, Tuple argumentTuple) {
+                if (constraint instanceof SymbolView<?> view) {
+                        new TypeConstraint(body, argumentTuple, getInputKey(view));
+                } else if (constraint instanceof Dnf dnf) {
+                        var calledPQuery = dnf2PQuery.translate(dnf);
+                        new PositivePatternCall(body, argumentTuple, calledPQuery);
+                } else {
+                        throw new IllegalArgumentException("Unknown Constraint: " + constraint);
+                }
+        }
+
+        public IInputKey getInputKey(AnySymbolView symbolView) {
+                return view2WrapperMap.computeIfAbsent(symbolView, SymbolViewWrapper::new);
+        }
+
+        public Map<AnySymbolView, IInputKey> getSymbolViews() {
+                return Collections.unmodifiableMap(view2WrapperMap);
+        }
+
+        public record WrappedCall(PQuery pattern, List<Variable> remappedArguments) {
+        }
+
+        private static class VariableAppender implements ToIntFunction<Variable> {
+                private final List<Variable> remappedArguments = new ArrayList<>();
+                private int nextIndex = 0;
+
+                @Override
+                public int applyAsInt(Variable variable) {
+                        remappedArguments.add(variable);
+                        int index = nextIndex;
+                        nextIndex++;
+                        return index;
+                }
+
+                public List<Variable> getRemappedArguments() {
+                        return remappedArguments;
+                }
+        }
+
+        private record RemappedConstraint(Constraint constraint, int[] remappedParameters) {
+                @Override
+                public boolean equals(Object o) {
+                        if (this == o) return true;
+                        if (o == null || getClass() != o.getClass()) return false;
+                        RemappedConstraint that = (RemappedConstraint) o;
+                        return constraint.equals(that.constraint) && Arrays.equals(remappedParameters, that.remappedParameters);
+                }
+
+                @Override
+                public int hashCode() {
+                        int result = Objects.hash(constraint);
+                        result = 31 * result + Arrays.hashCode(remappedParameters);
+                        return result;
+                }
+
+                @Override
+                public String toString() {
+                        return "RemappedConstraint{constraint=%s, remappedParameters=%s}".formatted(constraint,
+                                        Arrays.toString(remappedParameters));
+                }
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPQuery.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPQuery.java
index 71b74396..255738c5 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPQuery.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPQuery.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.pquery;
 
 import org.eclipse.viatra.query.runtime.api.GenericQuerySpecification;
@@ -9,6 +14,7 @@ import org.eclipse.viatra.query.runtime.matchers.psystem.queries.BasePQuery;
 import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PParameter;
 import org.eclipse.viatra.query.runtime.matchers.psystem.queries.PVisibility;
 import tools.refinery.store.query.viatra.internal.RelationalScope;
+import tools.refinery.store.query.viatra.internal.matcher.RawPatternMatcher;
 
 import java.util.LinkedHashSet;
 import java.util.List;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPatternMatcher.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPatternMatcher.java
deleted file mode 100644
index e944e873..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RawPatternMatcher.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package tools.refinery.store.query.viatra.internal.pquery;
-
-import org.eclipse.viatra.query.runtime.api.GenericPatternMatcher;
-import org.eclipse.viatra.query.runtime.api.GenericQuerySpecification;
-import tools.refinery.store.query.ResultSet;
-import tools.refinery.store.query.viatra.ViatraTupleLike;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.TupleLike;
-
-import java.util.Optional;
-import java.util.stream.Stream;
-
-public class RawPatternMatcher extends GenericPatternMatcher implements ResultSet {
-        protected final Object[] empty;
-
-        public RawPatternMatcher(GenericQuerySpecification<? extends GenericPatternMatcher> specification) {
-                super(specification);
-                empty = new Object[specification.getParameterNames().size()];
-        }
-
-        @Override
-        public boolean hasResult() {
-                return backend.hasMatch(empty);
-        }
-
-        @Override
-        public boolean hasResult(Tuple parameters) {
-                return backend.hasMatch(toParametersArray(parameters));
-        }
-
-        @Override
-        public Optional<TupleLike> oneResult() {
-                return backend.getOneArbitraryMatch(empty).map(ViatraTupleLike::new);
-        }
-
-        @Override
-        public Optional<TupleLike> oneResult(Tuple parameters) {
-                return backend.getOneArbitraryMatch(toParametersArray(parameters)).map(ViatraTupleLike::new);
-        }
-
-        @Override
-        public Stream<TupleLike> allResults() {
-                return backend.getAllMatches(empty).map(ViatraTupleLike::new);
-        }
-
-        @Override
-        public Stream<TupleLike> allResults(Tuple parameters) {
-                return backend.getAllMatches(toParametersArray(parameters)).map(ViatraTupleLike::new);
-        }
-
-        @Override
-        public int countResults() {
-                return backend.countMatches(empty);
-        }
-
-        @Override
-        public int countResults(Tuple parameters) {
-                return backend.countMatches(toParametersArray(parameters));
-        }
-
-        private Object[] toParametersArray(Tuple tuple) {
-                int size = tuple.getSize();
-                var array = new Object[tuple.getSize()];
-                for (int i = 0; i < size; i++) {
-                        var value = tuple.get(i);
-                        if (value >= 0) {
-                                array[i] = Tuple.of(value);
-                        }
-                }
-                return array;
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatefulMultisetAggregator.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatefulMultisetAggregator.java
new file mode 100644
index 00000000..461416f7
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatefulMultisetAggregator.java
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.IMultisetAggregationOperator;
+import tools.refinery.store.query.term.StatefulAggregate;
+import tools.refinery.store.query.term.StatefulAggregator;
+
+import java.util.stream.Stream;
+
+record StatefulMultisetAggregator<R, T>(StatefulAggregator<R, T> aggregator)
+        implements IMultisetAggregationOperator<T, StatefulAggregate<R, T>, R> {
+        @Override
+        public String getShortDescription() {
+                return getName();
+        }
+
+        @Override
+        public String getName() {
+                return aggregator.toString();
+        }
+
+        @Override
+        public StatefulAggregate<R, T> createNeutral() {
+                return aggregator.createEmptyAggregate();
+        }
+
+        @Override
+        public boolean isNeutral(StatefulAggregate<R, T> result) {
+                return result.isEmpty();
+        }
+
+        @Override
+        public StatefulAggregate<R, T> update(StatefulAggregate<R, T> oldResult, T updateValue, boolean isInsertion) {
+                if (isInsertion) {
+                        oldResult.add(updateValue);
+                } else {
+                        oldResult.remove(updateValue);
+                }
+                return oldResult;
+        }
+
+        @Override
+        public R getAggregate(StatefulAggregate<R, T> result) {
+                return result.getResult();
+        }
+
+        @Override
+        public R aggregateStream(Stream<T> stream) {
+                return aggregator.aggregateStream(stream);
+        }
+
+        @Override
+        public StatefulAggregate<R, T> clone(StatefulAggregate<R, T> original) {
+                return original.deepCopy();
+        }
+
+        @Override
+        public boolean contains(T value, StatefulAggregate<R, T> accumulator) {
+                return accumulator.contains(value);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatelessMultisetAggregator.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatelessMultisetAggregator.java
new file mode 100644
index 00000000..49175d75
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/StatelessMultisetAggregator.java
@@ -0,0 +1,55 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.psystem.aggregations.IMultisetAggregationOperator;
+import tools.refinery.store.query.term.StatelessAggregator;
+
+import java.util.stream.Stream;
+
+record StatelessMultisetAggregator<R, T>(StatelessAggregator<R, T> aggregator)
+                implements IMultisetAggregationOperator<T, R, R> {
+        @Override
+        public String getShortDescription() {
+                return getName();
+        }
+
+        @Override
+        public String getName() {
+                return aggregator.toString();
+        }
+
+        @Override
+        public R createNeutral() {
+                return aggregator.getEmptyResult();
+        }
+
+        @Override
+        public boolean isNeutral(R result) {
+                return createNeutral().equals(result);
+        }
+
+        @Override
+        public R update(R oldResult, T updateValue, boolean isInsertion) {
+                return isInsertion ? aggregator.add(oldResult, updateValue) : aggregator.remove(oldResult, updateValue);
+        }
+
+        @Override
+        public R getAggregate(R result) {
+                return result;
+        }
+
+        @Override
+        public R clone(R original) {
+                // Aggregate result is immutable.
+                return original;
+        }
+
+        @Override
+        public R aggregateStream(Stream<T> stream) {
+                return aggregator.aggregateStream(stream);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RelationViewWrapper.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/SymbolViewWrapper.java
index c442add8..a777613e 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/RelationViewWrapper.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/SymbolViewWrapper.java
@@ -1,10 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.pquery;
 
 import org.eclipse.viatra.query.runtime.matchers.context.common.BaseInputKeyWrapper;
-import tools.refinery.store.query.view.AnyRelationView;
+import tools.refinery.store.query.view.AnySymbolView;
 
-public class RelationViewWrapper extends BaseInputKeyWrapper<AnyRelationView> {
-        public RelationViewWrapper(AnyRelationView wrappedKey) {
+public class SymbolViewWrapper extends BaseInputKeyWrapper<AnySymbolView> {
+        public SymbolViewWrapper(AnySymbolView wrappedKey) {
                 super(wrappedKey);
         }
 
@@ -27,4 +32,9 @@ public class RelationViewWrapper extends BaseInputKeyWrapper<AnyRelationView> {
         public boolean isEnumerable() {
                 return true;
         }
+
+        @Override
+        public String toString() {
+                return "RelationViewWrapper{wrappedKey=%s}".formatted(wrappedKey);
+        }
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/TermEvaluator.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/TermEvaluator.java
new file mode 100644
index 00000000..1187f57a
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/TermEvaluator.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.psystem.IExpressionEvaluator;
+import org.eclipse.viatra.query.runtime.matchers.psystem.IValueProvider;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.stream.Collectors;
+
+class TermEvaluator<T> implements IExpressionEvaluator {
+        private final Term<T> term;
+
+        public TermEvaluator(Term<T> term) {
+                this.term = term;
+        }
+
+        @Override
+        public String getShortDescription() {
+                return term.toString();
+        }
+
+        @Override
+        public Iterable<String> getInputParameterNames() {
+                return term.getInputVariables().stream().map(Variable::getUniqueName).collect(Collectors.toUnmodifiableSet());
+        }
+
+        @Override
+        public Object evaluateExpression(IValueProvider provider) {
+                var valuation = new ValueProviderBasedValuation(provider);
+                return term.evaluate(valuation);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/ValueProviderBasedValuation.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/ValueProviderBasedValuation.java
new file mode 100644
index 00000000..62cb8b3a
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/pquery/ValueProviderBasedValuation.java
@@ -0,0 +1,19 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.pquery;
+
+import org.eclipse.viatra.query.runtime.matchers.psystem.IValueProvider;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.valuation.Valuation;
+
+public record ValueProviderBasedValuation(IValueProvider valueProvider) implements Valuation {
+        @Override
+        public <T> T getValue(DataVariable<T> variable) {
+                @SuppressWarnings("unchecked")
+                var value = (T) valueProvider.getValue(variable.getUniqueName());
+                return value;
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/ModelUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/ModelUpdateListener.java
index 8a467066..986bb0b1 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/ModelUpdateListener.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/ModelUpdateListener.java
@@ -1,47 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.update;
 
 import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
 import org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContextListener;
 import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
 import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
-import tools.refinery.store.query.view.AnyRelationView;
-import tools.refinery.store.query.view.RelationView;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.SymbolView;
 
 import java.util.HashMap;
 import java.util.Map;
 
 public class ModelUpdateListener {
-        private final Map<AnyRelationView, RelationViewUpdateListener<?>> relationViewUpdateListeners;
+        private final Map<AnySymbolView, SymbolViewUpdateListener<?>> symbolViewUpdateListeners;
 
         public ModelUpdateListener(ViatraModelQueryAdapterImpl adapter) {
-                var relationViews = adapter.getStoreAdapter().getInputKeys().keySet();
-                relationViewUpdateListeners = new HashMap<>(relationViews.size());
-                for (var relationView : relationViews) {
-                        registerView(adapter, (RelationView<?>) relationView);
+                var symbolViews = adapter.getStoreAdapter().getInputKeys().keySet();
+                symbolViewUpdateListeners = new HashMap<>(symbolViews.size());
+                for (var symbolView : symbolViews) {
+                        registerView(adapter, (SymbolView<?>) symbolView);
                 }
         }
 
-        private <T> void registerView(ViatraModelQueryAdapterImpl adapter, RelationView<T> relationView) {
-                var listener = RelationViewUpdateListener.of(adapter, relationView);
+        private <T> void registerView(ViatraModelQueryAdapterImpl adapter, SymbolView<T> view) {
                 var model = adapter.getModel();
-                var interpretation = model.getInterpretation(relationView.getSymbol());
-                interpretation.addListener(listener, true);
-                relationViewUpdateListeners.put(relationView, listener);
+                var interpretation = model.getInterpretation(view.getSymbol());
+                var listener = SymbolViewUpdateListener.of(adapter, view, interpretation);
+                symbolViewUpdateListeners.put(view, listener);
         }
 
-        public boolean containsRelationView(AnyRelationView relationView) {
-                return relationViewUpdateListeners.containsKey(relationView);
+        public boolean containsSymbolView(AnySymbolView relationView) {
+                return symbolViewUpdateListeners.containsKey(relationView);
         }
 
-        public void addListener(IInputKey key, AnyRelationView relationView, ITuple seed,
+        public void addListener(IInputKey key, AnySymbolView symbolView, ITuple seed,
                                                         IQueryRuntimeContextListener listener) {
-                var relationViewUpdateListener = relationViewUpdateListeners.get(relationView);
-                relationViewUpdateListener.addFilter(key, seed, listener);
+                var symbolViewUpdateListener = symbolViewUpdateListeners.get(symbolView);
+                symbolViewUpdateListener.addFilter(key, seed, listener);
         }
 
-        public void removeListener(IInputKey key, AnyRelationView relationView, ITuple seed,
+        public void removeListener(IInputKey key, AnySymbolView symbolView, ITuple seed,
                                                            IQueryRuntimeContextListener listener) {
-                var relationViewUpdateListener = relationViewUpdateListeners.get(relationView);
-                relationViewUpdateListener.removeFilter(key, seed, listener);
+                var symbolViewUpdateListener = symbolViewUpdateListeners.get(symbolView);
+                symbolViewUpdateListener.removeFilter(key, seed, listener);
         }
 }
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewFilter.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewFilter.java
index 221f1b4a..efdbfcbe 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewFilter.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewFilter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.update;
 
 import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewUpdateListener.java
deleted file mode 100644
index bf6b4197..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/RelationViewUpdateListener.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package tools.refinery.store.query.viatra.internal.update;
-
-import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
-import org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContextListener;
-import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
-import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
-import tools.refinery.store.model.InterpretationListener;
-import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
-import tools.refinery.store.query.view.RelationView;
-import tools.refinery.store.query.view.TuplePreservingRelationView;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public abstract class RelationViewUpdateListener<T> implements InterpretationListener<T> {
-        private final ViatraModelQueryAdapterImpl adapter;
-        private final List<RelationViewFilter> filters = new ArrayList<>();
-
-        protected RelationViewUpdateListener(ViatraModelQueryAdapterImpl adapter) {
-                this.adapter = adapter;
-        }
-
-        public void addFilter(IInputKey inputKey, ITuple seed, IQueryRuntimeContextListener listener) {
-                filters.add(new RelationViewFilter(inputKey, seed, listener));
-        }
-
-        public void removeFilter(IInputKey inputKey, ITuple seed, IQueryRuntimeContextListener listener) {
-                filters.remove(new RelationViewFilter(inputKey, seed, listener));
-        }
-
-        protected void processUpdate(Tuple tuple, boolean isInsertion) {
-                adapter.markAsPending();
-                int size = filters.size();
-                // Use a for loop instead of a for-each loop to avoid <code>Iterator</code> allocation overhead.
-                //noinspection ForLoopReplaceableByForEach
-                for (int i = 0; i < size; i++) {
-                        filters.get(i).update(tuple, isInsertion);
-                }
-        }
-
-        public static <T> RelationViewUpdateListener<T> of(ViatraModelQueryAdapterImpl adapter,
-                                                                                                           RelationView<T> relationView) {
-                if (relationView instanceof TuplePreservingRelationView<T> tuplePreservingRelationView) {
-                        return new TuplePreservingRelationViewUpdateListener<>(adapter, tuplePreservingRelationView);
-                }
-                return new TupleChangingRelationViewUpdateListener<>(adapter, relationView);
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/SymbolViewUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/SymbolViewUpdateListener.java
new file mode 100644
index 00000000..f1a2ac7c
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/SymbolViewUpdateListener.java
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.update;
+
+import org.eclipse.viatra.query.runtime.matchers.context.IInputKey;
+import org.eclipse.viatra.query.runtime.matchers.context.IQueryRuntimeContextListener;
+import org.eclipse.viatra.query.runtime.matchers.tuple.ITuple;
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuple;
+import tools.refinery.store.model.Interpretation;
+import tools.refinery.store.model.InterpretationListener;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
+import tools.refinery.store.query.view.SymbolView;
+import tools.refinery.store.query.view.TuplePreservingView;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public abstract class SymbolViewUpdateListener<T> implements InterpretationListener<T> {
+        private final ViatraModelQueryAdapterImpl adapter;
+        private final Interpretation<T> interpretation;
+        private final List<RelationViewFilter> filters = new ArrayList<>();
+
+        protected SymbolViewUpdateListener(ViatraModelQueryAdapterImpl adapter, Interpretation<T> interpretation) {
+                this.adapter = adapter;
+                this.interpretation = interpretation;
+        }
+
+        public void addFilter(IInputKey inputKey, ITuple seed, IQueryRuntimeContextListener listener) {
+                if (filters.isEmpty()) {
+                        // First filter to be added, from now on we have to subscribe to model updates.
+                        interpretation.addListener(this, true);
+                }
+                filters.add(new RelationViewFilter(inputKey, seed, listener));
+        }
+
+        public void removeFilter(IInputKey inputKey, ITuple seed, IQueryRuntimeContextListener listener) {
+                if (filters.remove(new RelationViewFilter(inputKey, seed, listener)) && filters.isEmpty()) {
+                        // Last listener to be added, we don't have be subscribed to model updates anymore.
+                        interpretation.removeListener(this);
+                }
+        }
+
+        protected void processUpdate(Tuple tuple, boolean isInsertion) {
+                adapter.markAsPending();
+                int size = filters.size();
+                // Use a for loop instead of a for-each loop to avoid <code>Iterator</code> allocation overhead.
+                //noinspection ForLoopReplaceableByForEach
+                for (int i = 0; i < size; i++) {
+                        filters.get(i).update(tuple, isInsertion);
+                }
+        }
+
+        public static <T> SymbolViewUpdateListener<T> of(ViatraModelQueryAdapterImpl adapter,
+                                                                                                         SymbolView<T> view,
+                                                                                                         Interpretation<T> interpretation) {
+                if (view instanceof TuplePreservingView<T> tuplePreservingRelationView) {
+                        return new TuplePreservingViewUpdateListener<>(adapter, tuplePreservingRelationView,
+                                        interpretation);
+                }
+                return new TupleChangingViewUpdateListener<>(adapter, view, interpretation);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingRelationViewUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingRelationViewUpdateListener.java
deleted file mode 100644
index 14142884..00000000
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingRelationViewUpdateListener.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package tools.refinery.store.query.viatra.internal.update;
-
-import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
-import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
-import tools.refinery.store.query.view.RelationView;
-import tools.refinery.store.tuple.Tuple;
-
-import java.util.Arrays;
-
-public class TupleChangingRelationViewUpdateListener<T> extends RelationViewUpdateListener<T> {
-        private final RelationView<T> relationView;
-
-        TupleChangingRelationViewUpdateListener(ViatraModelQueryAdapterImpl adapter, RelationView<T> relationView) {
-        super(adapter);
-        this.relationView = relationView;
-        }
-
-        @Override
-        public void put(Tuple key, T fromValue, T toValue, boolean restoring) {
-                boolean fromPresent = relationView.filter(key, fromValue);
-                boolean toPresent = relationView.filter(key, toValue);
-                if (fromPresent) {
-                        if (toPresent) { // value change
-                                var fromArray = relationView.forwardMap(key, fromValue);
-                                var toArray = relationView.forwardMap(key, toValue);
-                                if (!Arrays.equals(fromArray, toArray)) {
-                                        processUpdate(Tuples.flatTupleOf(fromArray), false);
-                                        processUpdate(Tuples.flatTupleOf(toArray), true);
-                                }
-                        } else { // fromValue disappears
-                                processUpdate(Tuples.flatTupleOf(relationView.forwardMap(key, fromValue)), false);
-                        }
-                } else if (toPresent) { // toValue appears
-                        processUpdate(Tuples.flatTupleOf(relationView.forwardMap(key, toValue)), true);
-                }
-        }
-}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingViewUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingViewUpdateListener.java
new file mode 100644
index 00000000..45d35571
--- /dev/null
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TupleChangingViewUpdateListener.java
@@ -0,0 +1,44 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.update;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import tools.refinery.store.model.Interpretation;
+import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
+import tools.refinery.store.query.view.SymbolView;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Arrays;
+
+public class TupleChangingViewUpdateListener<T> extends SymbolViewUpdateListener<T> {
+        private final SymbolView<T> view;
+
+        TupleChangingViewUpdateListener(ViatraModelQueryAdapterImpl adapter, SymbolView<T> view,
+                                                                        Interpretation<T> interpretation) {
+        super(adapter, interpretation);
+        this.view = view;
+        }
+
+        @Override
+        public void put(Tuple key, T fromValue, T toValue, boolean restoring) {
+                boolean fromPresent = view.filter(key, fromValue);
+                boolean toPresent = view.filter(key, toValue);
+                if (fromPresent) {
+                        if (toPresent) { // value change
+                                var fromArray = view.forwardMap(key, fromValue);
+                                var toArray = view.forwardMap(key, toValue);
+                                if (!Arrays.equals(fromArray, toArray)) {
+                                        processUpdate(Tuples.flatTupleOf(fromArray), false);
+                                        processUpdate(Tuples.flatTupleOf(toArray), true);
+                                }
+                        } else { // fromValue disappears
+                                processUpdate(Tuples.flatTupleOf(view.forwardMap(key, fromValue)), false);
+                        }
+                } else if (toPresent) { // toValue appears
+                        processUpdate(Tuples.flatTupleOf(view.forwardMap(key, toValue)), true);
+                }
+        }
+}
diff --git a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TuplePreservingRelationViewUpdateListener.java b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TuplePreservingViewUpdateListener.java
index 288e018a..c18dbafb 100644
--- a/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TuplePreservingRelationViewUpdateListener.java
+++ b/subprojects/store-query-viatra/src/main/java/tools/refinery/store/query/viatra/internal/update/TuplePreservingViewUpdateListener.java
@@ -1,16 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra.internal.update;
 
 import org.eclipse.viatra.query.runtime.matchers.tuple.Tuples;
+import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.query.viatra.internal.ViatraModelQueryAdapterImpl;
-import tools.refinery.store.query.view.TuplePreservingRelationView;
+import tools.refinery.store.query.view.TuplePreservingView;
 import tools.refinery.store.tuple.Tuple;
 
-public class TuplePreservingRelationViewUpdateListener<T> extends RelationViewUpdateListener<T> {
-        private final TuplePreservingRelationView<T> view;
+public class TuplePreservingViewUpdateListener<T> extends SymbolViewUpdateListener<T> {
+        private final TuplePreservingView<T> view;
 
-        TuplePreservingRelationViewUpdateListener(ViatraModelQueryAdapterImpl adapter,
-                                                                                          TuplePreservingRelationView<T> view) {
-        super(adapter);
+        TuplePreservingViewUpdateListener(ViatraModelQueryAdapterImpl adapter, TuplePreservingView<T> view,
+                                                                          Interpretation<T> interpretation) {
+        super(adapter, interpretation);
         this.view = view;
         }
 
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/DiagonalQueryTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/DiagonalQueryTest.java
new file mode 100644
index 00000000..6aae2ebe
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/DiagonalQueryTest.java
@@ -0,0 +1,390 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.viatra.tests.QueryEngineTest;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.FunctionView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.term.int_.IntTerms.INT_SUM;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertNullableResults;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertResults;
+
+class DiagonalQueryTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final Symbol<Boolean> symbol = Symbol.of("symbol", 4);
+        private static final Symbol<Integer> intSymbol = Symbol.of("intSymbol", 4, Integer.class);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final AnySymbolView symbolView = new KeyOnlyView<>(symbol);
+        private static final FunctionView<Integer> intSymbolView = new FunctionView<>(intSymbol);
+
+        @QueryEngineTest
+        void inputKeyNegationTest(QueryEvaluationHint hint) {
+                var query = Query.of("Diagonal", (builder, p1) -> builder.clause(p2 -> List.of(
+                                personView.call(p1),
+                                not(symbolView.call(p1, p1, p2, p2))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, symbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var symbolInterpretation = model.getInterpretation(symbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 1), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 2), true);
+                symbolInterpretation.put(Tuple.of(1, 1, 0, 1), true);
+                symbolInterpretation.put(Tuple.of(1, 2, 1, 1), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void subQueryNegationTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", (builder, p1, p2, p3, p4) -> builder
+                                .clause(
+                                                personView.call(p1),
+                                                symbolView.call(p1, p2, p3, p4)
+                                )
+                                .clause(
+                                                personView.call(p2),
+                                                symbolView.call(p1, p2, p3, p4)
+                                ));
+                var query = Query.of("Diagonal", (builder, p1) -> builder.clause(p2 -> List.of(
+                                personView.call(p1),
+                                not(subQuery.call(p1, p1, p2, p2))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, symbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var symbolInterpretation = model.getInterpretation(symbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 1), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 2), true);
+                symbolInterpretation.put(Tuple.of(1, 1, 0, 1), true);
+                symbolInterpretation.put(Tuple.of(1, 2, 1, 1), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void inputKeyCountTest(QueryEvaluationHint hint) {
+                var query = Query.of("Diagonal", Integer.class, (builder, p1, output) -> builder.clause(p2 -> List.of(
+                                personView.call(p1),
+                                output.assign(symbolView.count(p1, p1, p2, p2))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, symbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var symbolInterpretation = model.getInterpretation(symbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 1), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 2, 2), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 2), true);
+                symbolInterpretation.put(Tuple.of(1, 1, 0, 1), true);
+                symbolInterpretation.put(Tuple.of(1, 2, 1, 1), true);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(2),
+                                Tuple.of(1), Optional.of(0),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void subQueryCountTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", (builder, p1, p2, p3, p4) -> builder.clause(
+                                                personView.call(p1),
+                                                symbolView.call(p1, p2, p3, p4)
+                                )
+                                .clause(
+                                                personView.call(p2),
+                                                symbolView.call(p1, p2, p3, p4)
+                                ));
+                var query = Query.of("Diagonal", Integer.class, (builder, p1, output) -> builder.clause(p2 -> List.of(
+                                personView.call(p1),
+                                output.assign(subQuery.count(p1, p1, p2, p2))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, symbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var symbolInterpretation = model.getInterpretation(symbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 1), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 2, 2), true);
+                symbolInterpretation.put(Tuple.of(0, 0, 1, 2), true);
+                symbolInterpretation.put(Tuple.of(1, 1, 0, 1), true);
+                symbolInterpretation.put(Tuple.of(1, 2, 1, 1), true);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(2),
+                                Tuple.of(1), Optional.of(0),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void inputKeyAggregationTest(QueryEvaluationHint hint) {
+                var query = Query.of("Diagonal", Integer.class, (builder, p1, output) -> builder
+                                .clause((p2) -> List.of(
+                                                personView.call(p1),
+                                                output.assign(intSymbolView.aggregate(INT_SUM, p1, p1, p2, p2))
+                                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, intSymbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var intSymbolInterpretation = model.getInterpretation(intSymbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                intSymbolInterpretation.put(Tuple.of(0, 0, 1, 1), 1);
+                intSymbolInterpretation.put(Tuple.of(0, 0, 2, 2), 2);
+                intSymbolInterpretation.put(Tuple.of(0, 0, 1, 2), 10);
+                intSymbolInterpretation.put(Tuple.of(1, 1, 0, 1), 11);
+                intSymbolInterpretation.put(Tuple.of(1, 2, 1, 1), 12);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(3),
+                                Tuple.of(1), Optional.of(0),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void subQueryAggregationTest(QueryEvaluationHint hint) {
+                var subQuery = Dnf.of("SubQuery", builder -> {
+                        var p1 = builder.parameter("p1");
+                        var p2 = builder.parameter("p2");
+                        var p3 = builder.parameter("p3");
+                        var p4 = builder.parameter("p4");
+                        var x = builder.parameter("x", Integer.class);
+                        var y = builder.parameter("y", Integer.class);
+                        builder.clause(
+                                        personView.call(p1),
+                                        intSymbolView.call(p1, p2, p3, p4, x),
+                                        y.assign(x)
+                        );
+                        builder.clause(
+                                        personView.call(p2),
+                                        intSymbolView.call(p1, p2, p3, p4, x),
+                                        y.assign(x)
+                        );
+                });
+                var query = Query.of("Diagonal", Integer.class, (builder, p1, output) -> builder
+                                .clause(Integer.class, Integer.class, (p2, y, z) -> List.of(
+                                                personView.call(p1),
+                                                output.assign(subQuery.aggregateBy(y, INT_SUM, p1, p1, p2, p2, y, z))
+                                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, intSymbol)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var intSymbolInterpretation = model.getInterpretation(intSymbol);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                intSymbolInterpretation.put(Tuple.of(0, 0, 1, 1), 1);
+                intSymbolInterpretation.put(Tuple.of(0, 0, 2, 2), 2);
+                intSymbolInterpretation.put(Tuple.of(0, 0, 1, 2), 10);
+                intSymbolInterpretation.put(Tuple.of(1, 1, 0, 1), 11);
+                intSymbolInterpretation.put(Tuple.of(1, 2, 1, 1), 12);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(3),
+                                Tuple.of(1), Optional.of(0),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void inputKeyTransitiveTest(QueryEvaluationHint hint) {
+                var query = Query.of("Diagonal", (builder, p1) -> builder.clause(
+                                personView.call(p1),
+                                friendView.callTransitive(p1, p1)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                friendInterpretation.put(Tuple.of(0, 0), true);
+                friendInterpretation.put(Tuple.of(0, 1), true);
+                friendInterpretation.put(Tuple.of(1, 2), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void subQueryTransitiveTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", (builder, p1, p2) -> builder
+                                .clause(
+                                                personView.call(p1),
+                                                friendView.call(p1, p2)
+                                )
+                                .clause(
+                                                personView.call(p2),
+                                                friendView.call(p1, p2)
+                                ));
+                var query = Query.of("Diagonal", (builder, p1) -> builder.clause(
+                                personView.call(p1),
+                                subQuery.callTransitive(p1, p1)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                friendInterpretation.put(Tuple.of(0, 0), true);
+                friendInterpretation.put(Tuple.of(0, 1), true);
+                friendInterpretation.put(Tuple.of(1, 2), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), queryResultSet);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/FunctionalQueryTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/FunctionalQueryTest.java
new file mode 100644
index 00000000..258127e7
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/FunctionalQueryTest.java
@@ -0,0 +1,483 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.viatra.tests.QueryEngineTest;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.FilteredView;
+import tools.refinery.store.query.view.FunctionView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.nullValue;
+import static org.junit.jupiter.api.Assertions.assertAll;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.literal.Literals.assume;
+import static tools.refinery.store.query.term.int_.IntTerms.*;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertNullableResults;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertResults;
+
+class FunctionalQueryTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Integer> age = Symbol.of("age", 1, Integer.class);
+        private static final Symbol<TruthValue> friend = Symbol.of("friend", 2, TruthValue.class, TruthValue.FALSE);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final FunctionView<Integer> ageView = new FunctionView<>(age);
+        private static final AnySymbolView friendMustView = new FilteredView<>(friend, "must", TruthValue::must);
+
+        @QueryEngineTest
+        void inputKeyTest(QueryEvaluationHint hint) {
+                var query = Query.of("InputKey", Integer.class, (builder, p1, output) -> builder.clause(
+                                personView.call(p1),
+                                ageView.call(p1, output)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+                ageInterpretation.put(Tuple.of(2), 36);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(12),
+                                Tuple.of(1), Optional.of(24),
+                                Tuple.of(2), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void predicateTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", Integer.class, (builder, p1, x) -> builder.clause(
+                                personView.call(p1),
+                                ageView.call(p1, x)
+                ));
+                var query = Query.of("Predicate", Integer.class, (builder, p1, output) -> builder.clause(
+                                personView.call(p1),
+                                output.assign(subQuery.call(p1))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+                ageInterpretation.put(Tuple.of(2), 36);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(12),
+                                Tuple.of(1), Optional.of(24),
+                                Tuple.of(2), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void computationTest(QueryEvaluationHint hint) {
+                var query = Query.of("Computation", Integer.class, (builder, p1, output) -> builder.clause(() -> {
+                        var x = Variable.of("x", Integer.class);
+                        return List.of(
+                                        personView.call(p1),
+                                        ageView.call(p1, x),
+                                        output.assign(mul(x, constant(7)))
+                        );
+                }));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(84),
+                                Tuple.of(1), Optional.of(168),
+                                Tuple.of(2), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void inputKeyCountTest(QueryEvaluationHint hint) {
+                var query = Query.of("Count", Integer.class, (builder, p1, output) -> builder.clause(
+                                personView.call(p1),
+                                output.assign(friendMustView.count(p1, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(1),
+                                Tuple.of(1), Optional.of(2),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void predicateCountTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", (builder, p1, p2) -> builder.clause(
+                                        personView.call(p1),
+                                        personView.call(p2),
+                                        friendMustView.call(p1, p2)
+                ));
+                var query = Query.of("Count", Integer.class, (builder, p1, output) -> builder.clause(
+                                personView.call(p1),
+                                output.assign(subQuery.count(p1, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.of(1),
+                                Tuple.of(1), Optional.of(2),
+                                Tuple.of(2), Optional.of(0),
+                                Tuple.of(3), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void inputKeyAggregationTest(QueryEvaluationHint hint) {
+                var query = Query.of("Aggregate", Integer.class, (builder, output) -> builder.clause(
+                                output.assign(ageView.aggregate(INT_SUM, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(), 36), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void predicateAggregationTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", Integer.class, (builder, p1, x) -> builder.clause(
+                                personView.call(p1),
+                                ageView.call(p1, x)
+                ));
+                var query = Query.of("Aggregate", Integer.class, (builder, output) -> builder.clause(
+                                output.assign(subQuery.aggregate(INT_SUM, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(), 36), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void extremeValueTest(QueryEvaluationHint hint) {
+                var subQuery = Query.of("SubQuery", Integer.class, (builder, p1, x) -> builder.clause(
+                                personView.call(p1),
+                                x.assign(friendMustView.count(p1, Variable.of()))
+                ));
+                var minQuery = Query.of("Min", Integer.class, (builder, output) -> builder.clause(
+                                output.assign(subQuery.aggregate(INT_MIN, Variable.of()))
+                ));
+                var maxQuery = Query.of("Max", Integer.class, (builder, output) -> builder.clause(
+                                output.assign(subQuery.aggregate(INT_MAX, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(minQuery, maxQuery))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var minResultSet = queryEngine.getResultSet(minQuery);
+                var maxResultSet = queryEngine.getResultSet(maxQuery);
+
+                assertResults(Map.of(Tuple.of(), Integer.MAX_VALUE), minResultSet);
+                assertResults(Map.of(Tuple.of(), Integer.MIN_VALUE), maxResultSet);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(), 0), minResultSet);
+                assertResults(Map.of(Tuple.of(), 2), maxResultSet);
+
+                friendInterpretation.put(Tuple.of(2, 0), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(2, 1), TruthValue.TRUE);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(), 1), minResultSet);
+                assertResults(Map.of(Tuple.of(), 2), maxResultSet);
+
+                friendInterpretation.put(Tuple.of(0, 1), TruthValue.FALSE);
+                friendInterpretation.put(Tuple.of(1, 0), TruthValue.FALSE);
+                friendInterpretation.put(Tuple.of(2, 0), TruthValue.FALSE);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(), 0), minResultSet);
+                assertResults(Map.of(Tuple.of(), 1), maxResultSet);
+        }
+
+        @QueryEngineTest
+        void invalidComputationTest(QueryEvaluationHint hint) {
+                var query = Query.of("InvalidComputation", Integer.class,
+                                (builder, p1, output) -> builder.clause(Integer.class, (x) -> List.of(
+                                                personView.call(p1),
+                                                ageView.call(p1, x),
+                                                output.assign(div(constant(120), x))
+                                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 0);
+                ageInterpretation.put(Tuple.of(1), 30);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(
+                                Tuple.of(0), Optional.empty(),
+                                Tuple.of(1), Optional.of(4),
+                                Tuple.of(2), Optional.empty()
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void invalidAssumeTest(QueryEvaluationHint hint) {
+                var query = Query.of("InvalidAssume", (builder, p1) -> builder.clause(Integer.class, (x) -> List.of(
+                                personView.call(p1),
+                                ageView.call(p1, x),
+                                assume(lessEq(div(constant(120), x), constant(5)))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                ageInterpretation.put(Tuple.of(0), 0);
+                ageInterpretation.put(Tuple.of(1), 30);
+                ageInterpretation.put(Tuple.of(2), 20);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), queryResultSet);
+        }
+
+        @QueryEngineTest
+        void notFunctionalTest(QueryEvaluationHint hint) {
+                var query = Query.of("NotFunctional", Integer.class, (builder, p1, output) -> builder.clause((p2) -> List.of(
+                                personView.call(p1),
+                                friendMustView.call(p1, p2),
+                                ageView.call(p2, output)
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age, friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                ageInterpretation.put(Tuple.of(0), 24);
+                ageInterpretation.put(Tuple.of(1), 30);
+                ageInterpretation.put(Tuple.of(2), 36);
+
+                friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
+                friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
+
+                queryEngine.flushChanges();
+                var invalidTuple = Tuple.of(1);
+                var cursor = queryResultSet.getAll();
+                assertAll(
+                                () -> assertThat("value for key 0", queryResultSet.get(Tuple.of(0)), is(30)),
+                                () -> assertThrows(IllegalStateException.class, () -> queryResultSet.get(invalidTuple),
+                                                "multiple values for key 1"),
+                                () -> assertThat("value for key 2", queryResultSet.get(Tuple.of(2)), is(nullValue())),
+                                () -> assertThat("value for key 3", queryResultSet.get(Tuple.of(3)), is(nullValue()))
+                );
+                if (hint.getQueryBackendRequirementType() != QueryEvaluationHint.BackendRequirement.DEFAULT_SEARCH) {
+                        // Local search doesn't support throwing an error on multiple function return values.
+                        assertThat("results size", queryResultSet.size(), is(2));
+                        assertThrows(IllegalStateException.class, () -> enumerateValues(cursor), "move cursor");
+                }
+        }
+
+        private static void enumerateValues(Cursor<?, ?> cursor) {
+                //noinspection StatementWithEmptyBody
+                while (cursor.move()) {
+                        // Nothing do, just let the cursor move through the result set.
+                }
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/OrderedResultSetTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/OrderedResultSetTest.java
new file mode 100644
index 00000000..8ede6c80
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/OrderedResultSetTest.java
@@ -0,0 +1,117 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.resultset.OrderedResultSet;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+
+class OrderedResultSetTest {
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+
+        @Test
+        void relationalFlushTest() {
+                var query = Query.of("Relation", (builder, p1, p2) -> builder.clause(
+                                 friendView.call(p1, p2)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var resultSet = queryEngine.getResultSet(query);
+
+                friendInterpretation.put(Tuple.of(0, 1), true);
+                friendInterpretation.put(Tuple.of(1, 2), true);
+                friendInterpretation.put(Tuple.of(1, 1), true);
+                queryEngine.flushChanges();
+
+                try (var orderedResultSet = new OrderedResultSet<>(resultSet)) {
+                        assertThat(orderedResultSet.size(), is(3));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(0, 1)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(1, 1)));
+                        assertThat(orderedResultSet.getKey(2), is(Tuple.of(1, 2)));
+
+                        friendInterpretation.put(Tuple.of(1, 2), false);
+                        friendInterpretation.put(Tuple.of(0, 2), true);
+                        queryEngine.flushChanges();
+
+                        assertThat(orderedResultSet.size(), is(3));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(0, 1)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(0, 2)));
+                        assertThat(orderedResultSet.getKey(2), is(Tuple.of(1, 1)));
+                }
+        }
+
+        @Test
+        void functionalFlushTest() {
+                var query = Query.of("Function", Integer.class, (builder, p1, output) -> builder.clause(
+                                friendView.call(p1, Variable.of()),
+                                output.assign(friendView.count(p1, Variable.of()))
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(friend)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var friendInterpretation = model.getInterpretation(friend);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var resultSet = queryEngine.getResultSet(query);
+
+                friendInterpretation.put(Tuple.of(0, 1), true);
+                friendInterpretation.put(Tuple.of(1, 2), true);
+                friendInterpretation.put(Tuple.of(1, 1), true);
+                queryEngine.flushChanges();
+
+                try (var orderedResultSet = new OrderedResultSet<>(resultSet)) {
+                        assertThat(orderedResultSet.size(), is(2));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(0)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(1)));
+
+                        friendInterpretation.put(Tuple.of(0, 1), false);
+                        friendInterpretation.put(Tuple.of(2, 1), true);
+                        queryEngine.flushChanges();
+
+                        assertThat(orderedResultSet.size(), is(2));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(1)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(2)));
+
+                        friendInterpretation.put(Tuple.of(1, 1), false);
+                        queryEngine.flushChanges();
+
+                        assertThat(orderedResultSet.size(), is(2));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(1)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(2)));
+
+                        friendInterpretation.put(Tuple.of(1, 2), false);
+                        friendInterpretation.put(Tuple.of(1, 0), true);
+                        queryEngine.flushChanges();
+
+                        assertThat(orderedResultSet.size(), is(2));
+                        assertThat(orderedResultSet.getKey(0), is(Tuple.of(1)));
+                        assertThat(orderedResultSet.getKey(1), is(Tuple.of(2)));
+                }
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTest.java
index 6a37b54a..25bcb0dc 100644
--- a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTest.java
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTest.java
@@ -1,47 +1,57 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra;
 
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
 import org.junit.jupiter.api.Test;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.ModelQuery;
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.atom.*;
-import tools.refinery.store.query.view.FilteredRelationView;
-import tools.refinery.store.query.view.KeyOnlyRelationView;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.viatra.tests.QueryEngineTest;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.FilteredView;
+import tools.refinery.store.query.view.FunctionView;
+import tools.refinery.store.query.view.KeyOnlyView;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.representation.TruthValue;
 import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.TupleLike;
 
-import java.util.HashSet;
-import java.util.Set;
-import java.util.stream.Stream;
+import java.util.List;
+import java.util.Map;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static tools.refinery.store.query.literal.Literals.assume;
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.term.int_.IntTerms.constant;
+import static tools.refinery.store.query.term.int_.IntTerms.greaterEq;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertResults;
 
 class QueryTest {
-        @Test
-        void typeConstraintTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var asset = new Symbol<>("Asset", 1, Boolean.class, false);
-                var personView = new KeyOnlyRelationView<>(person);
-
-                var p1 = new Variable("p1");
-                var predicate = DNF.builder("TypeConstraint")
-                                .parameters(p1)
-                                .clause(new RelationViewAtom(personView, p1))
-                                .build();
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<TruthValue> friend = Symbol.of("friend", 2, TruthValue.class, TruthValue.FALSE);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendMustView = new FilteredView<>(friend, "must", TruthValue::must);
+
+        @QueryEngineTest
+        void typeConstraintTest(QueryEvaluationHint hint) {
+                var asset = Symbol.of("Asset", 1);
+
+                var predicate = Query.of("TypeConstraint", (builder, p1) -> builder.clause(personView.call(p1)));
 
                 var store = ModelStore.builder()
                                 .symbols(person, asset)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var assetInterpretation = model.getInterpretation(asset);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -51,42 +61,34 @@ class QueryTest {
                 assetInterpretation.put(Tuple.of(2), true);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0), Tuple.of(1)));
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void relationConstraintTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("RelationConstraint")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void relationConstraintTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("RelationConstraint", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
-                assertEquals(0, predicateResultSet.countResults());
-
                 personInterpretation.put(Tuple.of(0), true);
                 personInterpretation.put(Tuple.of(1), true);
                 personInterpretation.put(Tuple.of(2), true);
@@ -94,97 +96,36 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
                 friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
-
-                assertEquals(0, predicateResultSet.countResults());
+                friendInterpretation.put(Tuple.of(1, 3), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 1), Tuple.of(1, 0), Tuple.of(1, 2)));
+                assertResults(Map.of(
+                                Tuple.of(0, 1), true,
+                                Tuple.of(1, 0), true,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 1), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void andTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("RelationConstraint")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2),
-                                                new RelationViewAtom(friendMustView, p2, p1)
-                                )
-                                .build();
+        @QueryEngineTest
+        void existTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("Exists", (builder, p1) -> builder.clause((p2) -> List.of(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                )));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
-                var predicateResultSet = queryEngine.getResultSet(predicate);
-
-                assertEquals(0, predicateResultSet.countResults());
-
-                personInterpretation.put(Tuple.of(0), true);
-                personInterpretation.put(Tuple.of(1), true);
-                personInterpretation.put(Tuple.of(2), true);
-
-                friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
-                friendInterpretation.put(Tuple.of(0, 2), TruthValue.TRUE);
-
-                queryEngine.flushChanges();
-                assertEquals(0, predicateResultSet.countResults());
-
-                friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
-                queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 1), Tuple.of(1, 0)));
-
-                friendInterpretation.put(Tuple.of(2, 0), TruthValue.TRUE);
-                queryEngine.flushChanges();
-                assertEquals(4, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 1), Tuple.of(1, 0), Tuple.of(0, 2),
-                                Tuple.of(2, 0)));
-        }
-
-        @Test
-        void existTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("RelationConstraint")
-                                .parameters(p1)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
-
-                var store = ModelStore.builder()
-                                .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
-                                .build();
-
-                var model = store.createEmptyModel();
-                var personInterpretation = model.getInterpretation(person);
-                var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -194,50 +135,44 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(0, 1), TruthValue.TRUE);
                 friendInterpretation.put(Tuple.of(1, 0), TruthValue.TRUE);
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
-
-                assertEquals(0, predicateResultSet.countResults());
+                friendInterpretation.put(Tuple.of(3, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0), Tuple.of(1)));
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void orTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var animal = new Symbol<>("Animal", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var animalView = new KeyOnlyRelationView<>(animal);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("Or")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .clause(
-                                                new RelationViewAtom(animalView, p1),
-                                                new RelationViewAtom(animalView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void orTest(QueryEvaluationHint hint) {
+                var animal = Symbol.of("Animal", 1);
+                var animalView = new KeyOnlyView<>(animal);
+
+                var predicate = Query.of("Or", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ).clause(
+                                animalView.call(p1),
+                                animalView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, animal, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var animalInterpretation = model.getInterpretation(animal);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -252,35 +187,33 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(3, 0), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 1), Tuple.of(2, 3)));
+                assertResults(Map.of(
+                                Tuple.of(0, 1), true,
+                                Tuple.of(0, 2), false,
+                                Tuple.of(2, 3), true,
+                                Tuple.of(3, 0), false,
+                                Tuple.of(3, 2), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void equalityTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var personView = new KeyOnlyRelationView<>(person);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("Equality")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new EquivalenceAtom(p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void equalityTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("Equality", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                p1.isEquivalent(p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -288,41 +221,36 @@ class QueryTest {
                 personInterpretation.put(Tuple.of(2), true);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 0), Tuple.of(1, 1), Tuple.of(2, 2)));
+                assertResults(Map.of(
+                                Tuple.of(0, 0), true,
+                                Tuple.of(1, 1), true,
+                                Tuple.of(2, 2), true,
+                                Tuple.of(0, 1), false,
+                                Tuple.of(3, 3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void inequalityTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var p3 = new Variable("p3");
-                var predicate = DNF.builder("Inequality")
-                                .parameters(p1, p2, p3)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p3),
-                                                new RelationViewAtom(friendMustView, p2, p3),
-                                                new EquivalenceAtom(false, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void inequalityTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("Inequality", (builder, p1, p2, p3) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p3),
+                                friendMustView.call(p2, p3),
+                                p1.notEquivalent(p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -333,49 +261,37 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
-                compareMatchSets(predicateResultSet.allResults(), Set.of(Tuple.of(0, 1, 2), Tuple.of(1, 0, 2)));
+                assertResults(Map.of(
+                                Tuple.of(0, 1, 2), true,
+                                Tuple.of(1, 0, 2), true,
+                                Tuple.of(0, 0, 2), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void patternCallTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var friendPredicate = DNF.builder("RelationConstraint")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
-
-                var p3 = new Variable("p3");
-                var p4 = new Variable("p4");
-                var predicate = DNF.builder("PositivePatternCall")
-                                .parameters(p3, p4)
-                                .clause(
-                                                new RelationViewAtom(personView, p3),
-                                                new RelationViewAtom(personView, p4),
-                                                new DNFCallAtom(friendPredicate, p3, p4)
-                                )
-                                .build();
+        @QueryEngineTest
+        void patternCallTest(QueryEvaluationHint hint) {
+                var friendPredicate = Query.of("Friend", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
+                var predicate = Query.of("PositivePatternCall", (builder, p3, p4) -> builder.clause(
+                                personView.call(p3),
+                                personView.call(p4),
+                                friendPredicate.call(p3, p4)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -387,37 +303,33 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0, 1), true,
+                                Tuple.of(1, 0), true,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 1), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void negativeRelationViewTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("NegativePatternCall")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(false, friendMustView, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void negativeRelationViewTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("NegativePatternCall", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                not(friendMustView.call(p1, p2))
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -429,48 +341,44 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(6, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0, 0), true,
+                                Tuple.of(0, 2), true,
+                                Tuple.of(1, 1), true,
+                                Tuple.of(2, 0), true,
+                                Tuple.of(2, 1), true,
+                                Tuple.of(2, 2), true,
+                                Tuple.of(0, 1), false,
+                                Tuple.of(1, 0), false,
+                                Tuple.of(1, 2), false,
+                                Tuple.of(0, 3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void negativePatternCallTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var friendPredicate = DNF.builder("RelationConstraint")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
-
-                var p3 = new Variable("p3");
-                var p4 = new Variable("p4");
-                var predicate = DNF.builder("NegativePatternCall")
-                                .parameters(p3, p4)
-                                .clause(
-                                                new RelationViewAtom(personView, p3),
-                                                new RelationViewAtom(personView, p4),
-                                                new DNFCallAtom(false, friendPredicate, p3, p4)
-                                )
-                                .build();
+        @QueryEngineTest
+        void negativePatternCallTest(QueryEvaluationHint hint) {
+                var friendPredicate = Query.of("Friend", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
+                var predicate = Query.of("NegativePatternCall", (builder, p3, p4) -> builder.clause(
+                                personView.call(p3),
+                                personView.call(p4),
+                                not(friendPredicate.call(p3, p4))
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -482,37 +390,38 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(6, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0, 0), true,
+                                Tuple.of(0, 2), true,
+                                Tuple.of(1, 1), true,
+                                Tuple.of(2, 0), true,
+                                Tuple.of(2, 1), true,
+                                Tuple.of(2, 2), true,
+                                Tuple.of(0, 1), false,
+                                Tuple.of(1, 0), false,
+                                Tuple.of(1, 2), false,
+                                Tuple.of(0, 3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void negativeRelationViewWithQuantificationTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-
-                var predicate = DNF.builder("Count")
-                                .parameters(p1)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(false, friendMustView, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void negativeRelationViewWithQuantificationTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("Negative", (builder, p1) -> builder.clause(
+                                personView.call(p1),
+                                not(friendMustView.call(p1, Variable.of()))
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -523,46 +432,37 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(0, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void negativeWithQuantificationTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-
-                var called = DNF.builder("Called")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
-
-                var predicate = DNF.builder("Count")
-                                .parameters(p1)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new DNFCallAtom(false, called, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void negativeWithQuantificationTest(QueryEvaluationHint hint) {
+                var called = Query.of("Called", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
+                var predicate = Query.of("Negative", (builder, p1) -> builder.clause(
+                                personView.call(p1),
+                                not(called.call(p1, Variable.of()))
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -573,37 +473,33 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(0, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void transitiveRelationViewTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var predicate = DNF.builder("TransitivePatternCall")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(CallPolarity.TRANSITIVE, friendMustView, p1, p2)
-                                )
-                                .build();
+        @QueryEngineTest
+        void transitiveRelationViewTest(QueryEvaluationHint hint) {
+                var predicate = Query.of("Transitive", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.callTransitive(p1, p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -614,48 +510,44 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0, 0), false,
+                                Tuple.of(0, 1), true,
+                                Tuple.of(0, 2), true,
+                                Tuple.of(1, 0), false,
+                                Tuple.of(1, 1), false,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 0), false,
+                                Tuple.of(2, 1), false,
+                                Tuple.of(2, 2), false,
+                                Tuple.of(2, 3), false
+                ), predicateResultSet);
         }
 
-        @Test
-        void transitivePatternCallTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, TruthValue.class, TruthValue.FALSE);
-                var personView = new KeyOnlyRelationView<>(person);
-                var friendMustView = new FilteredRelationView<>(friend, "must", TruthValue::must);
-
-                var p1 = new Variable("p1");
-                var p2 = new Variable("p2");
-                var friendPredicate = DNF.builder("RelationConstraint")
-                                .parameters(p1, p2)
-                                .clause(
-                                                new RelationViewAtom(personView, p1),
-                                                new RelationViewAtom(personView, p2),
-                                                new RelationViewAtom(friendMustView, p1, p2)
-                                )
-                                .build();
-
-                var p3 = new Variable("p3");
-                var p4 = new Variable("p4");
-                var predicate = DNF.builder("TransitivePatternCall")
-                                .parameters(p3, p4)
-                                .clause(
-                                                new RelationViewAtom(personView, p3),
-                                                new RelationViewAtom(personView, p4),
-                                                new DNFCallAtom(CallPolarity.TRANSITIVE, friendPredicate, p3, p4)
-                                )
-                                .build();
+        @QueryEngineTest
+        void transitivePatternCallTest(QueryEvaluationHint hint) {
+                var called = Query.of("Called", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                friendMustView.call(p1, p2)
+                ));
+                var predicate = Query.of("Transitive", (builder, p1, p2) -> builder.clause(
+                                personView.call(p1),
+                                personView.call(p2),
+                                called.callTransitive(p1, p2)
+                ));
 
                 var store = ModelStore.builder()
                                 .symbols(person, friend)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var friendInterpretation = model.getInterpretation(friend);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -666,16 +558,150 @@ class QueryTest {
                 friendInterpretation.put(Tuple.of(1, 2), TruthValue.TRUE);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0, 0), false,
+                                Tuple.of(0, 1), true,
+                                Tuple.of(0, 2), true,
+                                Tuple.of(1, 0), false,
+                                Tuple.of(1, 1), false,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 0), false,
+                                Tuple.of(2, 1), false,
+                                Tuple.of(2, 2), false,
+                                Tuple.of(2, 3), false
+                ), predicateResultSet);
+        }
+
+        @Test
+        void filteredIntegerViewTest() {
+                var distance = Symbol.of("distance", 2, Integer.class);
+                var nearView = new FilteredView<>(distance, value -> value < 2);
+                var farView = new FilteredView<>(distance, value -> value >= 5);
+                var dangerQuery = Query.of("danger", (builder, a1, a2) -> builder.clause((a3) -> List.of(
+                                a1.notEquivalent(a2),
+                                nearView.call(a1, a3),
+                                nearView.call(a2, a3),
+                                not(farView.call(a1, a2))
+                )));
+                var store = ModelStore.builder()
+                                .symbols(distance)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(dangerQuery))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var distanceInterpretation = model.getInterpretation(distance);
+                distanceInterpretation.put(Tuple.of(0, 1), 1);
+                distanceInterpretation.put(Tuple.of(1, 0), 1);
+                distanceInterpretation.put(Tuple.of(0, 2), 1);
+                distanceInterpretation.put(Tuple.of(2, 0), 1);
+                distanceInterpretation.put(Tuple.of(1, 2), 3);
+                distanceInterpretation.put(Tuple.of(2, 1), 3);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var dangerResultSet = queryEngine.getResultSet(dangerQuery);
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0, 1), false,
+                                Tuple.of(0, 2), false,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 1), true
+                ), dangerResultSet);
+        }
+
+        @Test
+        void filteredDoubleViewTest() {
+                var distance = Symbol.of("distance", 2, Double.class);
+                var nearView = new FilteredView<>(distance, value -> value < 2);
+                var farView = new FilteredView<>(distance, value -> value >= 5);
+                var dangerQuery = Query.of("danger", (builder, a1, a2) -> builder.clause((a3) -> List.of(
+                                a1.notEquivalent(a2),
+                                nearView.call(a1, a3),
+                                nearView.call(a2, a3),
+                                not(farView.call(a1, a2))
+                )));
+                var store = ModelStore.builder()
+                                .symbols(distance)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(dangerQuery))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var distanceInterpretation = model.getInterpretation(distance);
+                distanceInterpretation.put(Tuple.of(0, 1), 1.0);
+                distanceInterpretation.put(Tuple.of(1, 0), 1.0);
+                distanceInterpretation.put(Tuple.of(0, 2), 1.0);
+                distanceInterpretation.put(Tuple.of(2, 0), 1.0);
+                distanceInterpretation.put(Tuple.of(1, 2), 3.0);
+                distanceInterpretation.put(Tuple.of(2, 1), 3.0);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var dangerResultSet = queryEngine.getResultSet(dangerQuery);
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0, 1), false,
+                                Tuple.of(0, 2), false,
+                                Tuple.of(1, 2), true,
+                                Tuple.of(2, 1), true
+                ), dangerResultSet);
+        }
+
+        @QueryEngineTest
+        void assumeTest(QueryEvaluationHint hint) {
+                var age = Symbol.of("age", 1, Integer.class);
+                var ageView = new FunctionView<>(age);
+
+                var query = Query.of("Constraint", (builder, p1) -> builder.clause(Integer.class, (x) -> List.of(
+                                personView.call(p1),
+                                ageView.call(p1, x),
+                                assume(greaterEq(x, constant(18)))
+                )));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .defaultHint(hint)
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                ageInterpretation.put(Tuple.of(0), 12);
+                ageInterpretation.put(Tuple.of(1), 24);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false
+                ), queryResultSet);
         }
 
-        static void compareMatchSets(Stream<TupleLike> matchSet, Set<Tuple> expected) {
-                Set<Tuple> translatedMatchSet = new HashSet<>();
-                var iterator = matchSet.iterator();
-                while (iterator.hasNext()) {
-                        var element = iterator.next();
-                        translatedMatchSet.add(element.toTuple());
-                }
-                assertEquals(expected, translatedMatchSet);
+        @Test
+        void alwaysFalseTest() {
+                var predicate = Query.of("AlwaysFalse", builder -> builder.parameter("p1"));
+
+                var store = ModelStore.builder()
+                                .symbols(person)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(predicate))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var predicateResultSet = queryEngine.getResultSet(predicate);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+                personInterpretation.put(Tuple.of(2), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(), predicateResultSet);
         }
 }
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTransactionTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTransactionTest.java
index 98995339..66f043c6 100644
--- a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTransactionTest.java
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/QueryTransactionTest.java
@@ -1,43 +1,163 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.viatra;
 
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.ModelQuery;
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.atom.RelationViewAtom;
-import tools.refinery.store.query.view.KeyOnlyRelationView;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.FilteredView;
+import tools.refinery.store.query.view.FunctionView;
+import tools.refinery.store.query.view.KeyOnlyView;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple;
 
-import static org.junit.jupiter.api.Assertions.*;
+import java.util.Map;
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertNullableResults;
+import static tools.refinery.store.query.viatra.tests.QueryAssertions.assertResults;
 
 class QueryTransactionTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Integer> age = Symbol.of("age", 1, Integer.class);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView ageView = new FunctionView<>(age);
+        private static final RelationalQuery predicate = Query.of("TypeConstraint", (builder, p1) ->
+                        builder.clause(personView.call(p1)));
+
         @Test
         void flushTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var asset = new Symbol<>("Asset", 1, Boolean.class, false);
-                var personView = new KeyOnlyRelationView<>(person);
-
-                var p1 = new Variable("p1");
-                var predicate = DNF.builder("TypeConstraint")
-                                .parameters(p1)
-                                .clause(new RelationViewAtom(personView, p1))
+                var store = ModelStore.builder()
+                                .symbols(person)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(predicate))
                                 .build();
 
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var predicateResultSet = queryEngine.getResultSet(predicate);
+
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertTrue(queryEngine.hasPendingChanges());
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+
+                personInterpretation.put(Tuple.of(1), false);
+                personInterpretation.put(Tuple.of(2), true);
+
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertTrue(queryEngine.hasPendingChanges());
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), false,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+        }
+
+        @Test
+        void localSearchTest() {
+                var store = ModelStore.builder()
+                                .symbols(person)
+                                .with(ViatraModelQueryAdapter.builder()
+                                        .defaultHint(new QueryEvaluationHint(null, QueryEvaluationHint.BackendRequirement.DEFAULT_SEARCH))
+                                        .queries(predicate))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var predicateResultSet = queryEngine.getResultSet(predicate);
+
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+
+                personInterpretation.put(Tuple.of(1), false);
+                personInterpretation.put(Tuple.of(2), true);
+
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), false,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+        }
+
+        @Test
+        void unrelatedChangesTest() {
+                var asset = Symbol.of("Asset", 1);
+
                 var store = ModelStore.builder()
                                 .symbols(person, asset)
-                                .with(ViatraModelQuery.ADAPTER)
-                                .queries(predicate)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(predicate))
                                 .build();
 
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
                 var assetInterpretation = model.getInterpretation(asset);
-                var queryEngine = model.getAdapter(ModelQuery.ADAPTER);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
                 var predicateResultSet = queryEngine.getResultSet(predicate);
 
-                assertEquals(0, predicateResultSet.countResults());
                 assertFalse(queryEngine.hasPendingChanges());
 
                 personInterpretation.put(Tuple.of(0), true);
@@ -46,19 +166,208 @@ class QueryTransactionTest {
                 assetInterpretation.put(Tuple.of(1), true);
                 assetInterpretation.put(Tuple.of(2), true);
 
-                assertEquals(0, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0), false,
+                                Tuple.of(1), false,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false,
+                                Tuple.of(4), false
+                ), predicateResultSet);
                 assertTrue(queryEngine.hasPendingChanges());
 
                 queryEngine.flushChanges();
-                assertEquals(2, predicateResultSet.countResults());
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false,
+                                Tuple.of(4), false
+                ), predicateResultSet);
                 assertFalse(queryEngine.hasPendingChanges());
 
-                personInterpretation.put(Tuple.of(4), true);
-                assertEquals(2, predicateResultSet.countResults());
-                assertTrue(queryEngine.hasPendingChanges());
+                assetInterpretation.put(Tuple.of(3), true);
+                assertFalse(queryEngine.hasPendingChanges());
+
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false,
+                                Tuple.of(4), false
+                ), predicateResultSet);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false,
+                                Tuple.of(4), false
+                ), predicateResultSet);
+                assertFalse(queryEngine.hasPendingChanges());
+        }
+
+        @Test
+        void tupleChangingChangeTest() {
+                var query = Query.of("TypeConstraint", Integer.class, (builder, p1, output) -> builder.clause(
+                                personView.call(p1),
+                                ageView.call(p1, output)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+
+                ageInterpretation.put(Tuple.of(0), 24);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(0), 24), queryResultSet);
+
+                ageInterpretation.put(Tuple.of(0), 25);
 
                 queryEngine.flushChanges();
-                assertEquals(3, predicateResultSet.countResults());
+                assertResults(Map.of(Tuple.of(0), 25), queryResultSet);
+
+                ageInterpretation.put(Tuple.of(0), null);
+
+                queryEngine.flushChanges();
+                assertNullableResults(Map.of(Tuple.of(0), Optional.empty()), queryResultSet);
+        }
+
+        @Test
+        void tuplePreservingUnchangedTest() {
+                var adultView = new FilteredView<>(age, "adult", n -> n != null && n >= 18);
+
+                var query = Query.of("TypeConstraint", (builder, p1) -> builder.clause(
+                                personView.call(p1),
+                                adultView.call(p1)
+                ));
+
+                var store = ModelStore.builder()
+                                .symbols(person, age)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(query))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var ageInterpretation = model.getInterpretation(age);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var queryResultSet = queryEngine.getResultSet(query);
+
+                personInterpretation.put(Tuple.of(0), true);
+
+                ageInterpretation.put(Tuple.of(0), 24);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(0), true), queryResultSet);
+
+                ageInterpretation.put(Tuple.of(0), 25);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(0), true), queryResultSet);
+
+                ageInterpretation.put(Tuple.of(0), 17);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(Tuple.of(0), false), queryResultSet);
+        }
+
+        @Disabled("TODO Fix DiffCursor")
+        @Test
+        void commitAfterFlushTest() {
+                var store = ModelStore.builder()
+                                .symbols(person)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(predicate))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var predicateResultSet = queryEngine.getResultSet(predicate);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+
+                var state1 = model.commit();
+
+                personInterpretation.put(Tuple.of(1), false);
+                personInterpretation.put(Tuple.of(2), true);
+
+                queryEngine.flushChanges();
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), false,
+                                Tuple.of(2), true,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+
+                model.restore(state1);
+
+                assertFalse(queryEngine.hasPendingChanges());
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
+        }
+
+        @Disabled("TODO Fix DiffCursor")
+        @Test
+        void commitWithoutFlushTest() {
+                var store = ModelStore.builder()
+                                .symbols(person)
+                                .with(ViatraModelQueryAdapter.builder()
+                                                .queries(predicate))
+                                .build();
+
+                var model = store.createEmptyModel();
+                var personInterpretation = model.getInterpretation(person);
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                var predicateResultSet = queryEngine.getResultSet(predicate);
+
+                personInterpretation.put(Tuple.of(0), true);
+                personInterpretation.put(Tuple.of(1), true);
+
+                assertResults(Map.of(), predicateResultSet);
+                assertTrue(queryEngine.hasPendingChanges());
+
+                var state1 = model.commit();
+
+                personInterpretation.put(Tuple.of(1), false);
+                personInterpretation.put(Tuple.of(2), true);
+
+                assertResults(Map.of(), predicateResultSet);
+                assertTrue(queryEngine.hasPendingChanges());
+
+                model.restore(state1);
+
+                assertResults(Map.of(
+                                Tuple.of(0), true,
+                                Tuple.of(1), true,
+                                Tuple.of(2), false,
+                                Tuple.of(3), false
+                ), predicateResultSet);
                 assertFalse(queryEngine.hasPendingChanges());
         }
 }
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperatorTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperatorTest.java
deleted file mode 100644
index 20dad543..00000000
--- a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperatorTest.java
+++ /dev/null
@@ -1,87 +0,0 @@
-package tools.refinery.store.query.viatra.internal.cardinality;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.equalTo;
-
-class UpperCardinalitySumAggregationOperatorTest {
-        private UpperCardinalitySumAggregationOperator.Accumulator accumulator;
-
-        @BeforeEach
-        void beforeEach() {
-                accumulator = UpperCardinalitySumAggregationOperator.INSTANCE.createNeutral();
-        }
-
-        @Test
-        void emptyAggregationTest() {
-                assertResult(UpperCardinality.of(0));
-        }
-
-        @Test
-        void singleBoundedTest() {
-                insert(UpperCardinality.of(3));
-                assertResult(UpperCardinality.of(3));
-        }
-
-        @Test
-        void multipleBoundedTest() {
-                insert(UpperCardinality.of(2));
-                insert(UpperCardinality.of(3));
-                assertResult(UpperCardinality.of(5));
-        }
-
-        @Test
-        void singleUnboundedTest() {
-                insert(UpperCardinalities.UNBOUNDED);
-                assertResult(UpperCardinalities.UNBOUNDED);
-        }
-
-        @Test
-        void multipleUnboundedTest() {
-                insert(UpperCardinalities.UNBOUNDED);
-                insert(UpperCardinalities.UNBOUNDED);
-                assertResult(UpperCardinalities.UNBOUNDED);
-        }
-
-        @Test
-        void removeBoundedTest() {
-                insert(UpperCardinality.of(2));
-                insert(UpperCardinality.of(3));
-                remove(UpperCardinality.of(2));
-                assertResult(UpperCardinality.of(3));
-        }
-
-        @Test
-        void removeAllUnboundedTest() {
-                insert(UpperCardinalities.UNBOUNDED);
-                insert(UpperCardinality.of(3));
-                remove(UpperCardinalities.UNBOUNDED);
-                assertResult(UpperCardinality.of(3));
-        }
-
-        @Test
-        void removeSomeUnboundedTest() {
-                insert(UpperCardinalities.UNBOUNDED);
-                insert(UpperCardinalities.UNBOUNDED);
-                insert(UpperCardinality.of(3));
-                remove(UpperCardinalities.UNBOUNDED);
-                assertResult(UpperCardinalities.UNBOUNDED);
-        }
-
-        private void insert(UpperCardinality value) {
-                accumulator = UpperCardinalitySumAggregationOperator.INSTANCE.update(accumulator, value, true);
-        }
-
-        private void remove(UpperCardinality value) {
-                accumulator = UpperCardinalitySumAggregationOperator.INSTANCE.update(accumulator, value, false);
-        }
-
-        private void assertResult(UpperCardinality expected) {
-                var result = UpperCardinalitySumAggregationOperator.INSTANCE.getAggregate(accumulator);
-                assertThat(result, equalTo(expected));
-        }
-}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtilsTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtilsTest.java
new file mode 100644
index 00000000..968c6c5e
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/matcher/MatcherUtilsTest.java
@@ -0,0 +1,239 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.internal.matcher;
+
+import org.eclipse.viatra.query.runtime.matchers.tuple.*;
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.*;
+
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.*;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+class MatcherUtilsTest {
+        @Test
+        void toViatra0Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of());
+                assertThat(viatraTuple.getSize(), is(0));
+                assertThat(viatraTuple, instanceOf(FlatTuple0.class));
+        }
+
+        @Test
+        void toViatra1Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of(2));
+                assertThat(viatraTuple.getSize(), is(1));
+                assertThat(viatraTuple.get(0), is(Tuple.of(2)));
+                assertThat(viatraTuple, instanceOf(FlatTuple1.class));
+        }
+
+        @Test
+        void toViatra2Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of(2, 3));
+                assertThat(viatraTuple.getSize(), is(2));
+                assertThat(viatraTuple.get(0), is(Tuple.of(2)));
+                assertThat(viatraTuple.get(1), is(Tuple.of(3)));
+                assertThat(viatraTuple, instanceOf(FlatTuple2.class));
+        }
+
+        @Test
+        void toViatra3Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of(2, 3, 5));
+                assertThat(viatraTuple.getSize(), is(3));
+                assertThat(viatraTuple.get(0), is(Tuple.of(2)));
+                assertThat(viatraTuple.get(1), is(Tuple.of(3)));
+                assertThat(viatraTuple.get(2), is(Tuple.of(5)));
+                assertThat(viatraTuple, instanceOf(FlatTuple3.class));
+        }
+
+        @Test
+        void toViatra4Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of(2, 3, 5, 8));
+                assertThat(viatraTuple.getSize(), is(4));
+                assertThat(viatraTuple.get(0), is(Tuple.of(2)));
+                assertThat(viatraTuple.get(1), is(Tuple.of(3)));
+                assertThat(viatraTuple.get(2), is(Tuple.of(5)));
+                assertThat(viatraTuple.get(3), is(Tuple.of(8)));
+                assertThat(viatraTuple, instanceOf(FlatTuple4.class));
+        }
+
+        @Test
+        void toViatra5Test() {
+                var viatraTuple = MatcherUtils.toViatraTuple(Tuple.of(2, 3, 5, 8, 13));
+                assertThat(viatraTuple.getSize(), is(5));
+                assertThat(viatraTuple.get(0), is(Tuple.of(2)));
+                assertThat(viatraTuple.get(1), is(Tuple.of(3)));
+                assertThat(viatraTuple.get(2), is(Tuple.of(5)));
+                assertThat(viatraTuple.get(3), is(Tuple.of(8)));
+                assertThat(viatraTuple.get(4), is(Tuple.of(13)));
+                assertThat(viatraTuple, instanceOf(FlatTuple.class));
+        }
+
+        @Test
+        void toRefinery0Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf());
+                assertThat(refineryTuple.getSize(), is(0));
+                assertThat(refineryTuple, instanceOf(Tuple0.class));
+        }
+
+        @Test
+        void toRefinery1Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf(Tuple.of(2)));
+                assertThat(refineryTuple.getSize(), is(1));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple, instanceOf(Tuple1.class));
+        }
+
+        @Test
+        void toRefinery2Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3)));
+                assertThat(refineryTuple.getSize(), is(2));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple, instanceOf(Tuple2.class));
+        }
+
+        @Test
+        void toRefinery3Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5)));
+                assertThat(refineryTuple.getSize(), is(3));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple, instanceOf(Tuple3.class));
+        }
+
+        @Test
+        void toRefinery4Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5),
+                                Tuple.of(8)));
+                assertThat(refineryTuple.getSize(), is(4));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple.get(3), is(8));
+                assertThat(refineryTuple, instanceOf(Tuple4.class));
+        }
+
+        @Test
+        void toRefinery5Test() {
+                var refineryTuple = MatcherUtils.toRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5),
+                                Tuple.of(8), Tuple.of(13)));
+                assertThat(refineryTuple.getSize(), is(5));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple.get(3), is(8));
+                assertThat(refineryTuple.get(4), is(13));
+                assertThat(refineryTuple, instanceOf(TupleN.class));
+        }
+
+        @Test
+        void toRefineryInvalidValueTest() {
+                var viatraTuple = Tuples.flatTupleOf(Tuple.of(2), -98);
+                assertThrows(IllegalArgumentException.class, () -> MatcherUtils.toRefineryTuple(viatraTuple));
+        }
+
+        @Test
+        void keyToRefinery0Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(-99));
+                assertThat(refineryTuple.getSize(), is(0));
+                assertThat(refineryTuple, instanceOf(Tuple0.class));
+        }
+
+        @Test
+        void keyToRefinery1Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), -99));
+                assertThat(refineryTuple.getSize(), is(1));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple, instanceOf(Tuple1.class));
+        }
+
+        @Test
+        void keyToRefinery2Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), -99));
+                assertThat(refineryTuple.getSize(), is(2));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple, instanceOf(Tuple2.class));
+        }
+
+        @Test
+        void keyToRefinery3Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5),
+                                -99));
+                assertThat(refineryTuple.getSize(), is(3));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple, instanceOf(Tuple3.class));
+        }
+
+        @Test
+        void keyToRefinery4Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5),
+                                Tuple.of(8), -99));
+                assertThat(refineryTuple.getSize(), is(4));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple.get(3), is(8));
+                assertThat(refineryTuple, instanceOf(Tuple4.class));
+        }
+
+        @Test
+        void keyToRefinery5Test() {
+                var refineryTuple = MatcherUtils.keyToRefineryTuple(Tuples.flatTupleOf(Tuple.of(2), Tuple.of(3), Tuple.of(5),
+                                Tuple.of(8), Tuple.of(13), -99));
+                assertThat(refineryTuple.getSize(), is(5));
+                assertThat(refineryTuple.get(0), is(2));
+                assertThat(refineryTuple.get(1), is(3));
+                assertThat(refineryTuple.get(2), is(5));
+                assertThat(refineryTuple.get(3), is(8));
+                assertThat(refineryTuple.get(4), is(13));
+                assertThat(refineryTuple, instanceOf(TupleN.class));
+        }
+
+        @Test
+        void keyToRefineryTooShortTest() {
+                var viatraTuple = Tuples.flatTupleOf();
+                assertThrows(IllegalArgumentException.class, () -> MatcherUtils.keyToRefineryTuple(viatraTuple));
+        }
+
+        @Test
+        void keyToRefineryInvalidValueTest() {
+                var viatraTuple = Tuples.flatTupleOf(Tuple.of(2), -98, -99);
+                assertThrows(IllegalArgumentException.class, () -> MatcherUtils.keyToRefineryTuple(viatraTuple));
+        }
+
+        @Test
+        void getSingleValueTest() {
+                var value = MatcherUtils.getSingleValue(List.of(Tuples.flatTupleOf(Tuple.of(2), -99)));
+                assertThat(value, is(-99));
+        }
+
+        // Static analysis accurately determines that the result is always {@code null}, but we check anyways.
+        @SuppressWarnings("ConstantValue")
+        @Test
+        void getSingleValueNullTest() {
+                var value = MatcherUtils.getSingleValue((Iterable<? extends ITuple>) null);
+                assertThat(value, nullValue());
+        }
+
+        @Test
+        void getSingleValueEmptyTest() {
+                var value = MatcherUtils.getSingleValue(List.of());
+                assertThat(value, nullValue());
+        }
+
+        @Test
+        void getSingleValueMultipleTest() {
+                var viatraTuples = List.of(Tuples.flatTupleOf(Tuple.of(2), -98), Tuples.flatTupleOf(Tuple.of(2), -99));
+                assertThrows(IllegalStateException.class, () -> MatcherUtils.getSingleValue(viatraTuples));
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryAssertions.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryAssertions.java
new file mode 100644
index 00000000..ca089a9d
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryAssertions.java
@@ -0,0 +1,57 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.tests;
+
+import org.junit.jupiter.api.function.Executable;
+import tools.refinery.store.query.resultset.ResultSet;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.*;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.nullValue;
+import static org.junit.jupiter.api.Assertions.assertAll;
+
+public final class QueryAssertions {
+        private QueryAssertions() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static <T> void assertNullableResults(Map<Tuple, Optional<T>> expected, ResultSet<T> resultSet) {
+                var nullableValuesMap = new LinkedHashMap<Tuple, T>(expected.size());
+                for (var entry : expected.entrySet()) {
+                        nullableValuesMap.put(entry.getKey(), entry.getValue().orElse(null));
+                }
+                assertResults(nullableValuesMap, resultSet);
+        }
+
+        public static <T> void assertResults(Map<Tuple, T> expected, ResultSet<T> resultSet) {
+                var defaultValue = resultSet.getQuery().defaultValue();
+                var filteredExpected = new LinkedHashMap<Tuple, T>();
+                var executables = new ArrayList<Executable>();
+                for (var entry : expected.entrySet()) {
+                        var key = entry.getKey();
+                        var value = entry.getValue();
+                        if (!Objects.equals(value, defaultValue)) {
+                                filteredExpected.put(key, value);
+                        }
+                        executables.add(() -> assertThat("value for key " + key,resultSet.get(key), is(value)));
+                }
+                executables.add(() -> assertThat("results size", resultSet.size(), is(filteredExpected.size())));
+
+                var actual = new LinkedHashMap<Tuple, T>();
+                var cursor = resultSet.getAll();
+                while (cursor.move()) {
+                        var key = cursor.getKey();
+                        var previous = actual.put(key, cursor.getValue());
+                        assertThat("duplicate value for key " + key, previous, nullValue());
+                }
+                executables.add(() -> assertThat("results cursor", actual, is(filteredExpected)));
+
+                assertAll(executables);
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryBackendHint.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryBackendHint.java
new file mode 100644
index 00000000..dc0e92c8
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryBackendHint.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.tests;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+
+/**
+ * Overrides {@link QueryEvaluationHint#toString()} for pretty names in parametric test names.
+ */
+class QueryBackendHint extends QueryEvaluationHint {
+        public QueryBackendHint(BackendRequirement backendRequirementType) {
+                super(null, backendRequirementType);
+        }
+
+        @Override
+        public String toString() {
+                return switch (getQueryBackendRequirementType()) {
+                        case UNSPECIFIED -> "default";
+                        case DEFAULT_CACHING -> "incremental";
+                        case DEFAULT_SEARCH -> "localSearch";
+                        default -> throw new IllegalStateException("Unknown BackendRequirement");
+                };
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEngineTest.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEngineTest.java
new file mode 100644
index 00000000..d4f16da7
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEngineTest.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.tests;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ArgumentsSource;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+@ParameterizedTest(name = "backend = {0}")
+@ArgumentsSource(QueryEvaluationHintSource.class)
+@Target(ElementType.METHOD)
+@Retention(RetentionPolicy.RUNTIME)
+public @interface QueryEngineTest {
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEvaluationHintSource.java b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEvaluationHintSource.java
new file mode 100644
index 00000000..9e75d5f3
--- /dev/null
+++ b/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/tests/QueryEvaluationHintSource.java
@@ -0,0 +1,24 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.viatra.tests;
+
+import org.eclipse.viatra.query.runtime.matchers.backend.QueryEvaluationHint;
+import org.junit.jupiter.api.extension.ExtensionContext;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.ArgumentsProvider;
+
+import java.util.stream.Stream;
+
+public class QueryEvaluationHintSource implements ArgumentsProvider {
+        @Override
+        public Stream<? extends Arguments> provideArguments(ExtensionContext context) {
+                return Stream.of(
+                                Arguments.of(new QueryBackendHint(QueryEvaluationHint.BackendRequirement.UNSPECIFIED)),
+                                Arguments.of(new QueryBackendHint(QueryEvaluationHint.BackendRequirement.DEFAULT_CACHING)),
+                                Arguments.of(new QueryBackendHint(QueryEvaluationHint.BackendRequirement.DEFAULT_SEARCH))
+                );
+        }
+}
diff --git a/subprojects/store-query/build.gradle.kts b/subprojects/store-query/build.gradle.kts
new file mode 100644
index 00000000..4d8e2605
--- /dev/null
+++ b/subprojects/store-query/build.gradle.kts
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+        id("tools.refinery.gradle.java-test-fixtures")
+}
+
+dependencies {
+        api(project(":refinery-store"))
+        testFixturesApi(libs.hamcrest)
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
new file mode 100644
index 00000000..916fb35c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
@@ -0,0 +1,72 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.literal.*;
+import tools.refinery.store.query.term.*;
+
+import java.util.List;
+
+public interface Constraint {
+        String name();
+
+        List<Parameter> getParameters();
+
+        default int arity() {
+                return getParameters().size();
+        }
+
+        default boolean invalidIndex(int i) {
+                return i < 0 || i >= arity();
+        }
+
+        default Reduction getReduction() {
+                return Reduction.NOT_REDUCIBLE;
+        }
+
+        default boolean equals(LiteralEqualityHelper helper, Constraint other) {
+                return equals(other);
+        }
+
+        default String toReferenceString() {
+                return name();
+        }
+
+        default CallLiteral call(CallPolarity polarity, List<Variable> arguments) {
+                return new CallLiteral(polarity, this, arguments);
+        }
+
+        default CallLiteral call(CallPolarity polarity, Variable... arguments) {
+                return call(polarity, List.of(arguments));
+        }
+
+        default CallLiteral call(Variable... arguments) {
+                return call(CallPolarity.POSITIVE, arguments);
+        }
+
+        default CallLiteral callTransitive(NodeVariable left, NodeVariable right) {
+                return call(CallPolarity.TRANSITIVE, List.of(left, right));
+        }
+
+        default AssignedValue<Integer> count(List<Variable> arguments) {
+                return targetVariable -> new CountLiteral(targetVariable, this, arguments);
+        }
+
+        default AssignedValue<Integer> count(Variable... arguments) {
+                return count(List.of(arguments));
+        }
+
+        default <R, T> AssignedValue<R> aggregateBy(DataVariable<T> inputVariable, Aggregator<R, T> aggregator,
+                                                                                                List<Variable> arguments) {
+                return targetVariable -> new AggregationLiteral<>(targetVariable, aggregator, inputVariable, this, arguments);
+        }
+
+        default <R, T> AssignedValue<R> aggregateBy(DataVariable<T> inputVariable, Aggregator<R, T> aggregator,
+                                                                                                Variable... arguments) {
+                return aggregateBy(inputVariable, aggregator, List.of(arguments));
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
new file mode 100644
index 00000000..1fa96a07
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
@@ -0,0 +1,26 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query;
+
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.resultset.AnyResultSet;
+import tools.refinery.store.query.resultset.ResultSet;
+
+public interface ModelQueryAdapter extends ModelAdapter {
+        ModelQueryStoreAdapter getStoreAdapter();
+
+        default AnyResultSet getResultSet(AnyQuery query) {
+                return getResultSet((Query<?>) query);
+        }
+
+        <T> ResultSet<T> getResultSet(Query<T> query);
+
+        boolean hasPendingChanges();
+
+        void flushChanges();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
new file mode 100644
index 00000000..c62a95b5
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query;
+
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.dnf.AnyQuery;
+
+import java.util.Collection;
+import java.util.List;
+
+@SuppressWarnings("UnusedReturnValue")
+public interface ModelQueryBuilder extends ModelAdapterBuilder {
+        default ModelQueryBuilder queries(AnyQuery... queries) {
+                return queries(List.of(queries));
+        }
+
+        default ModelQueryBuilder queries(Collection<? extends AnyQuery> queries) {
+                queries.forEach(this::query);
+                return this;
+        }
+
+        ModelQueryBuilder query(AnyQuery query);
+
+        @Override
+        ModelQueryStoreAdapter build(ModelStore store);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
new file mode 100644
index 00000000..f0a950a6
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query;
+
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.view.AnySymbolView;
+
+import java.util.Collection;
+
+public interface ModelQueryStoreAdapter extends ModelStoreAdapter {
+        Collection<AnySymbolView> getSymbolViews();
+
+        Collection<AnyQuery> getQueries();
+
+        @Override
+        ModelQueryAdapter createModelAdapter(Model model);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java
new file mode 100644
index 00000000..2a3e3ce0
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java
@@ -0,0 +1,175 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.dnf.callback.*;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+
+public abstract class AbstractQueryBuilder<T extends AbstractQueryBuilder<T>> {
+        protected final DnfBuilder dnfBuilder;
+
+        protected AbstractQueryBuilder(DnfBuilder dnfBuilder) {
+                this.dnfBuilder = dnfBuilder;
+        }
+
+        protected abstract T self();
+
+        public NodeVariable parameter() {
+                return dnfBuilder.parameter();
+        }
+
+        public NodeVariable parameter(String name) {
+                return dnfBuilder.parameter(name);
+        }
+
+        public NodeVariable parameter(ParameterDirection direction) {
+                return dnfBuilder.parameter(direction);
+        }
+
+        public NodeVariable parameter(String name, ParameterDirection direction) {
+                return dnfBuilder.parameter(name, direction);
+        }
+
+        public T parameter(NodeVariable variable) {
+                dnfBuilder.parameter(variable);
+                return self();
+        }
+
+        public T parameter(NodeVariable variable, ParameterDirection direction) {
+                dnfBuilder.parameter(variable, direction);
+                return self();
+        }
+
+        public T parameters(NodeVariable... variables) {
+                dnfBuilder.parameters(variables);
+                return self();
+        }
+
+        public T parameters(List<NodeVariable> variables) {
+                dnfBuilder.parameters(variables);
+                return self();
+        }
+
+        public T parameters(List<NodeVariable> variables, ParameterDirection direction) {
+                dnfBuilder.parameters(variables, direction);
+                return self();
+        }
+
+        public T symbolicParameters(List<SymbolicParameter> parameters) {
+                dnfBuilder.symbolicParameters(parameters);
+                return self();
+        }
+
+        public T functionalDependencies(Collection<FunctionalDependency<Variable>> functionalDependencies) {
+                dnfBuilder.functionalDependencies(functionalDependencies);
+                return self();
+        }
+
+        public T functionalDependency(FunctionalDependency<Variable> functionalDependency) {
+                dnfBuilder.functionalDependency(functionalDependency);
+                return self();
+        }
+
+        public T functionalDependency(Set<? extends Variable> forEach, Set<? extends Variable> unique) {
+                dnfBuilder.functionalDependency(forEach, unique);
+                return self();
+        }
+
+        public T clause(ClauseCallback0 callback) {
+                dnfBuilder.clause(callback);
+                return self();
+        }
+
+        public T clause(ClauseCallback1Data0 callback) {
+                dnfBuilder.clause(callback);
+                return self();
+        }
+
+        public <U1> T clause(Class<U1> type1, ClauseCallback1Data1<U1> callback) {
+                dnfBuilder.clause(type1, callback);
+                return self();
+        }
+
+        public T clause(ClauseCallback2Data0 callback) {
+                dnfBuilder.clause(callback);
+                return self();
+        }
+
+        public <U1> T clause(Class<U1> type1, ClauseCallback2Data1<U1> callback) {
+                dnfBuilder.clause(type1, callback);
+                return self();
+        }
+
+        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback2Data2<U1, U2> callback) {
+                dnfBuilder.clause(type1, type2, callback);
+                return self();
+        }
+
+        public T clause(ClauseCallback3Data0 callback) {
+                dnfBuilder.clause(callback);
+                return self();
+        }
+
+        public <U1> T clause(Class<U1> type1, ClauseCallback3Data1<U1> callback) {
+                dnfBuilder.clause(type1, callback);
+                return self();
+        }
+
+        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback3Data2<U1, U2> callback) {
+                dnfBuilder.clause(type1, type2, callback);
+                return self();
+        }
+
+        public <U1, U2, U3> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3,
+                                                                 ClauseCallback3Data3<U1, U2, U3> callback) {
+                dnfBuilder.clause(type1, type2, type3, callback);
+                return self();
+        }
+
+        public T clause(ClauseCallback4Data0 callback) {
+                dnfBuilder.clause(callback);
+                return self();
+        }
+
+        public <U1> T clause(Class<U1> type1, ClauseCallback4Data1<U1> callback) {
+                dnfBuilder.clause(type1, callback);
+                return self();
+        }
+
+        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback4Data2<U1, U2> callback) {
+                dnfBuilder.clause(type1, type2, callback);
+                return self();
+        }
+
+        public <U1, U2, U3> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3,
+                                                                 ClauseCallback4Data3<U1, U2, U3> callback) {
+                dnfBuilder.clause(type1, type2, type3, callback);
+                return self();
+        }
+
+        public <U1, U2, U3, U4> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3, Class<U4> type4,
+                                                                         ClauseCallback4Data4<U1, U2, U3, U4> callback) {
+                dnfBuilder.clause(type1, type2, type3, type4, callback);
+                return self();
+        }
+
+        public T clause(Literal... literals) {
+                dnfBuilder.clause(literals);
+                return self();
+        }
+
+        public T clause(Collection<? extends Literal> literals) {
+                dnfBuilder.clause(literals);
+                return self();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java
new file mode 100644
index 00000000..5e28af68
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+public sealed interface AnyQuery permits Query {
+        String name();
+
+        int arity();
+
+        Class<?> valueType();
+
+        Dnf getDnf();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
new file mode 100644
index 00000000..b5e7092b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
@@ -0,0 +1,324 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.jetbrains.annotations.NotNull;
+import tools.refinery.store.query.literal.BooleanLiteral;
+import tools.refinery.store.query.literal.EquivalenceLiteral;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.substitution.MapBasedSubstitution;
+import tools.refinery.store.query.substitution.StatelessSubstitution;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.*;
+import java.util.function.Function;
+
+class ClausePostProcessor {
+        private final Map<Variable, ParameterInfo> parameters;
+        private final List<Literal> literals;
+        private final Map<NodeVariable, NodeVariable> representatives = new LinkedHashMap<>();
+        private final Map<NodeVariable, Set<NodeVariable>> equivalencePartition = new HashMap<>();
+        private List<Literal> substitutedLiterals;
+        private final Set<Variable> existentiallyQuantifiedVariables = new LinkedHashSet<>();
+        private Set<Variable> positiveVariables;
+        private Map<Variable, Set<SortableLiteral>> variableToLiteralInputMap;
+        private PriorityQueue<SortableLiteral> literalsWithAllInputsBound;
+        private LinkedHashSet<Literal> topologicallySortedLiterals;
+
+        public ClausePostProcessor(Map<Variable, ParameterInfo> parameters, List<Literal> literals) {
+                this.parameters = parameters;
+                this.literals = literals;
+        }
+
+        public Result postProcessClause() {
+                mergeEquivalentNodeVariables();
+                substitutedLiterals = new ArrayList<>(literals.size());
+                keepParameterEquivalences();
+                substituteLiterals();
+                computeExistentiallyQuantifiedVariables();
+                computePositiveVariables();
+                validatePositiveRepresentatives();
+                validatePrivateVariables();
+                topologicallySortLiterals();
+                var filteredLiterals = new ArrayList<Literal>(topologicallySortedLiterals.size());
+                for (var literal : topologicallySortedLiterals) {
+                        var reducedLiteral = literal.reduce();
+                        if (BooleanLiteral.FALSE.equals(reducedLiteral)) {
+                                return ConstantResult.ALWAYS_FALSE;
+                        } else if (!BooleanLiteral.TRUE.equals(reducedLiteral)) {
+                                filteredLiterals.add(reducedLiteral);
+                        }
+                }
+                if (filteredLiterals.isEmpty()) {
+                        return ConstantResult.ALWAYS_TRUE;
+                }
+                var clause = new DnfClause(Collections.unmodifiableSet(positiveVariables),
+                                Collections.unmodifiableList(filteredLiterals));
+                return new ClauseResult(clause);
+        }
+
+        private void mergeEquivalentNodeVariables() {
+                for (var literal : literals) {
+                        if (isPositiveEquivalence(literal)) {
+                                var equivalenceLiteral = (EquivalenceLiteral) literal;
+                                mergeVariables(equivalenceLiteral.left(), equivalenceLiteral.right());
+                        }
+                }
+        }
+
+        private static boolean isPositiveEquivalence(Literal literal) {
+                return literal instanceof EquivalenceLiteral equivalenceLiteral && equivalenceLiteral.positive();
+        }
+
+        private void mergeVariables(NodeVariable left, NodeVariable right) {
+                var leftRepresentative = getRepresentative(left);
+                var rightRepresentative = getRepresentative(right);
+                var leftInfo = parameters.get(leftRepresentative);
+                var rightInfo = parameters.get(rightRepresentative);
+                if (leftInfo != null && (rightInfo == null || leftInfo.index() <= rightInfo.index())) {
+                        // Prefer the variable occurring earlier in the parameter list as a representative.
+                        doMergeVariables(leftRepresentative, rightRepresentative);
+                } else {
+                        doMergeVariables(rightRepresentative, leftRepresentative);
+                }
+        }
+
+        private void doMergeVariables(NodeVariable parentRepresentative, NodeVariable newChildRepresentative) {
+                var parentSet = getEquivalentVariables(parentRepresentative);
+                var childSet = getEquivalentVariables(newChildRepresentative);
+                parentSet.addAll(childSet);
+                equivalencePartition.remove(newChildRepresentative);
+                for (var childEquivalentNodeVariable : childSet) {
+                        representatives.put(childEquivalentNodeVariable, parentRepresentative);
+                }
+        }
+
+        private NodeVariable getRepresentative(NodeVariable variable) {
+                return representatives.computeIfAbsent(variable, Function.identity());
+        }
+
+        private Set<NodeVariable> getEquivalentVariables(NodeVariable variable) {
+                var representative = getRepresentative(variable);
+                if (!representative.equals(variable)) {
+                        throw new AssertionError("NodeVariable %s already has a representative %s"
+                                        .formatted(variable, representative));
+                }
+                return equivalencePartition.computeIfAbsent(variable, key -> {
+                        var set = new HashSet<NodeVariable>(1);
+                        set.add(key);
+                        return set;
+                });
+        }
+
+        private void keepParameterEquivalences() {
+                for (var pair : representatives.entrySet()) {
+                        var left = pair.getKey();
+                        var right = pair.getValue();
+                        if (!left.equals(right) && parameters.containsKey(left) && parameters.containsKey(right)) {
+                                substitutedLiterals.add(left.isEquivalent(right));
+                        }
+                }
+        }
+
+        private void substituteLiterals() {
+                Substitution substitution;
+                if (representatives.isEmpty()) {
+                        substitution = null;
+                } else {
+                        substitution = new MapBasedSubstitution(Collections.unmodifiableMap(representatives),
+                                        StatelessSubstitution.IDENTITY);
+                }
+                for (var literal : literals) {
+                        if (isPositiveEquivalence(literal)) {
+                                // We already retained all equivalences that cannot be replaced with substitutions in
+                                // {@link#keepParameterEquivalences()}.
+                                continue;
+                        }
+                        var substitutedLiteral = substitution == null ? literal : literal.substitute(substitution);
+                        substitutedLiterals.add(substitutedLiteral);
+                }
+        }
+
+        private void computeExistentiallyQuantifiedVariables() {
+                for (var literal : substitutedLiterals) {
+                        for (var variable : literal.getOutputVariables()) {
+                                boolean added = existentiallyQuantifiedVariables.add(variable);
+                                if (!variable.isUnifiable()) {
+                                        var parameterInfo = parameters.get(variable);
+                                        if (parameterInfo != null && parameterInfo.direction() == ParameterDirection.IN) {
+                                                throw new IllegalArgumentException("Trying to bind %s parameter %s"
+                                                                .formatted(ParameterDirection.IN, variable));
+                                        }
+                                        if (!added) {
+                                                throw new IllegalArgumentException("Variable %s has multiple assigned values"
+                                                                .formatted(variable));
+                                        }
+                                }
+                        }
+                }
+        }
+
+        private void computePositiveVariables() {
+                positiveVariables = new LinkedHashSet<>();
+                for (var pair : parameters.entrySet()) {
+                        var variable = pair.getKey();
+                        if (pair.getValue().direction() == ParameterDirection.IN) {
+                                // Inputs count as positive, because they are already bound when we evaluate literals.
+                                positiveVariables.add(variable);
+                        } else if (!existentiallyQuantifiedVariables.contains(variable)) {
+                                throw new IllegalArgumentException("Unbound %s parameter %s"
+                                                .formatted(ParameterDirection.OUT, variable));
+                        }
+                }
+                positiveVariables.addAll(existentiallyQuantifiedVariables);
+        }
+
+        private void validatePositiveRepresentatives() {
+                for (var pair : equivalencePartition.entrySet()) {
+                        var representative = pair.getKey();
+                        if (!positiveVariables.contains(representative)) {
+                                var variableSet = pair.getValue();
+                                throw new IllegalArgumentException("Variables %s were merged by equivalence but are not bound"
+                                                .formatted(variableSet));
+                        }
+                }
+        }
+
+        private void validatePrivateVariables() {
+                var negativeVariablesMap = new HashMap<Variable, Literal>();
+                for (var literal : substitutedLiterals) {
+                        for (var variable : literal.getPrivateVariables(positiveVariables)) {
+                                var oldLiteral = negativeVariablesMap.put(variable, literal);
+                                if (oldLiteral != null) {
+                                        throw new IllegalArgumentException("Unbound variable %s appears in multiple literals %s and %s"
+                                                        .formatted(variable, oldLiteral, literal));
+                                }
+                        }
+                }
+        }
+
+        private void topologicallySortLiterals() {
+                topologicallySortedLiterals = new LinkedHashSet<>(substitutedLiterals.size());
+                variableToLiteralInputMap = new HashMap<>();
+                literalsWithAllInputsBound = new PriorityQueue<>();
+                int size = substitutedLiterals.size();
+                for (int i = 0; i < size; i++) {
+                        var literal = substitutedLiterals.get(i);
+                        var sortableLiteral = new SortableLiteral(i, literal);
+                        sortableLiteral.enqueue();
+                }
+                while (!literalsWithAllInputsBound.isEmpty()) {
+                        var variable = literalsWithAllInputsBound.remove();
+                        variable.addToSortedLiterals();
+                }
+                if (!variableToLiteralInputMap.isEmpty()) {
+                        throw new IllegalArgumentException("Unbound input variables %s"
+                                        .formatted(variableToLiteralInputMap.keySet()));
+                }
+        }
+
+        private class SortableLiteral implements Comparable<SortableLiteral> {
+                private final int index;
+                private final Literal literal;
+                private final Set<Variable> remainingInputs;
+
+                private SortableLiteral(int index, Literal literal) {
+                        this.index = index;
+                        this.literal = literal;
+                        remainingInputs = new HashSet<>(literal.getInputVariables(positiveVariables));
+                        for (var pair : parameters.entrySet()) {
+                                if (pair.getValue().direction() == ParameterDirection.IN) {
+                                        remainingInputs.remove(pair.getKey());
+                                }
+                        }
+                }
+
+                public void enqueue() {
+                        if (allInputsBound()) {
+                                addToAllInputsBoundQueue();
+                        } else {
+                                addToVariableToLiteralInputMap();
+                        }
+                }
+
+                private void bindVariable(Variable input) {
+                        if (!remainingInputs.remove(input)) {
+                                throw new AssertionError("Already processed input %s of literal %s".formatted(input, literal));
+                        }
+                        if (allInputsBound()) {
+                                addToAllInputsBoundQueue();
+                        }
+                }
+
+                private boolean allInputsBound() {
+                        return remainingInputs.isEmpty();
+                }
+
+                private void addToVariableToLiteralInputMap() {
+                        for (var inputVariable : remainingInputs) {
+                                var literalSetForInput = variableToLiteralInputMap.computeIfAbsent(
+                                                inputVariable, key -> new HashSet<>());
+                                literalSetForInput.add(this);
+                        }
+                }
+
+                private void addToAllInputsBoundQueue() {
+                        literalsWithAllInputsBound.add(this);
+                }
+
+                public void addToSortedLiterals() {
+                        if (!allInputsBound()) {
+                                throw new AssertionError("Inputs %s of %s are not yet bound".formatted(remainingInputs, literal));
+                        }
+                        // Add literal if we haven't yet added a duplicate of this literal.
+                        topologicallySortedLiterals.add(literal);
+                        for (var variable : literal.getOutputVariables()) {
+                                var literalSetForInput = variableToLiteralInputMap.remove(variable);
+                                if (literalSetForInput == null) {
+                                        continue;
+                                }
+                                for (var targetSortableLiteral : literalSetForInput) {
+                                        targetSortableLiteral.bindVariable(variable);
+                                }
+                        }
+                }
+
+                @Override
+                public int compareTo(@NotNull ClausePostProcessor.SortableLiteral other) {
+                        return Integer.compare(index, other.index);
+                }
+
+                @Override
+                public boolean equals(Object o) {
+                        if (this == o) return true;
+                        if (o == null || getClass() != o.getClass()) return false;
+                        SortableLiteral that = (SortableLiteral) o;
+                        return index == that.index && Objects.equals(literal, that.literal);
+                }
+
+                @Override
+                public int hashCode() {
+                        return Objects.hash(index, literal);
+                }
+        }
+
+        public sealed interface Result permits ClauseResult, ConstantResult {
+        }
+
+        public record ClauseResult(DnfClause clause) implements Result {
+        }
+
+        public enum ConstantResult implements Result {
+                ALWAYS_TRUE,
+                ALWAYS_FALSE
+        }
+
+        public record ParameterInfo(ParameterDirection direction, int index) {
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java
new file mode 100644
index 00000000..50b245f7
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java
@@ -0,0 +1,213 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.literal.Reduction;
+import tools.refinery.store.query.equality.DnfEqualityChecker;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import java.util.function.Consumer;
+import java.util.stream.Collectors;
+
+public final class Dnf implements Constraint {
+        private static final String INDENTATION = "    ";
+
+        private final String name;
+        private final String uniqueName;
+        private final List<SymbolicParameter> symbolicParameters;
+        private final List<FunctionalDependency<Variable>> functionalDependencies;
+        private final List<DnfClause> clauses;
+
+        Dnf(String name, List<SymbolicParameter> symbolicParameters,
+                List<FunctionalDependency<Variable>> functionalDependencies, List<DnfClause> clauses) {
+                validateFunctionalDependencies(symbolicParameters, functionalDependencies);
+                this.name = name;
+                this.uniqueName = DnfUtils.generateUniqueName(name);
+                this.symbolicParameters = symbolicParameters;
+                this.functionalDependencies = functionalDependencies;
+                this.clauses = clauses;
+        }
+
+        private static void validateFunctionalDependencies(
+                        Collection<SymbolicParameter> symbolicParameters,
+                        Collection<FunctionalDependency<Variable>> functionalDependencies) {
+                var parameterSet = symbolicParameters.stream().map(SymbolicParameter::getVariable).collect(Collectors.toSet());
+                for (var functionalDependency : functionalDependencies) {
+                        validateParameters(symbolicParameters, parameterSet, functionalDependency.forEach(), functionalDependency);
+                        validateParameters(symbolicParameters, parameterSet, functionalDependency.unique(), functionalDependency);
+                }
+        }
+
+        private static void validateParameters(Collection<SymbolicParameter> symbolicParameters,
+                                                                                   Set<Variable> parameterSet, Collection<Variable> toValidate,
+                                                                                   FunctionalDependency<Variable> functionalDependency) {
+                for (var variable : toValidate) {
+                        if (!parameterSet.contains(variable)) {
+                                throw new IllegalArgumentException(
+                                                "Variable %s of functional dependency %s does not appear in the parameter list %s"
+                                                                .formatted(variable, functionalDependency, symbolicParameters));
+                        }
+                }
+        }
+
+        @Override
+        public String name() {
+                return name == null ? uniqueName : name;
+        }
+
+        public boolean isExplicitlyNamed() {
+                return name == null;
+        }
+
+        public String getUniqueName() {
+                return uniqueName;
+        }
+
+        public List<SymbolicParameter> getSymbolicParameters() {
+                return symbolicParameters;
+        }
+
+        public List<Parameter> getParameters() {
+                return Collections.unmodifiableList(symbolicParameters);
+        }
+
+        public List<FunctionalDependency<Variable>> getFunctionalDependencies() {
+                return functionalDependencies;
+        }
+
+        @Override
+        public int arity() {
+                return symbolicParameters.size();
+        }
+
+        public List<DnfClause> getClauses() {
+                return clauses;
+        }
+
+        public RelationalQuery asRelation() {
+                return new RelationalQuery(this);
+        }
+
+        public <T> FunctionalQuery<T> asFunction(Class<T> type) {
+                return new FunctionalQuery<>(this, type);
+        }
+
+        @Override
+        public Reduction getReduction() {
+                if (clauses.isEmpty()) {
+                        return Reduction.ALWAYS_FALSE;
+                }
+                for (var clause : clauses) {
+                        if (clause.literals().isEmpty()) {
+                                return Reduction.ALWAYS_TRUE;
+                        }
+                }
+                return Reduction.NOT_REDUCIBLE;
+        }
+
+        public boolean equalsWithSubstitution(DnfEqualityChecker callEqualityChecker, Dnf other) {
+                if (arity() != other.arity()) {
+                        return false;
+                }
+                for (int i = 0; i < arity(); i++) {
+                        if (!symbolicParameters.get(i).getDirection().equals(other.getSymbolicParameters().get(i).getDirection())) {
+                                return false;
+                        }
+                }
+                int numClauses = clauses.size();
+                if (numClauses != other.clauses.size()) {
+                        return false;
+                }
+                for (int i = 0; i < numClauses; i++) {
+                        var literalEqualityHelper = new LiteralEqualityHelper(callEqualityChecker, symbolicParameters,
+                                        other.symbolicParameters);
+                        if (!clauses.get(i).equalsWithSubstitution(literalEqualityHelper, other.clauses.get(i))) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+
+        @Override
+        public boolean equals(LiteralEqualityHelper helper, Constraint other) {
+                if (other instanceof Dnf otherDnf) {
+                        return helper.dnfEqual(this, otherDnf);
+                }
+                return false;
+        }
+
+        @Override
+        public String toString() {
+                return "%s/%d".formatted(name(), arity());
+        }
+
+        @Override
+        public String toReferenceString() {
+                return "@Dnf " + name();
+        }
+
+        public String toDefinitionString() {
+                var builder = new StringBuilder();
+                builder.append("pred ").append(name()).append("(");
+                var parameterIterator = symbolicParameters.iterator();
+                if (parameterIterator.hasNext()) {
+                        builder.append(parameterIterator.next());
+                        while (parameterIterator.hasNext()) {
+                                builder.append(", ").append(parameterIterator.next());
+                        }
+                }
+                builder.append(") <->");
+                var clauseIterator = clauses.iterator();
+                if (clauseIterator.hasNext()) {
+                        appendClause(clauseIterator.next(), builder);
+                        while (clauseIterator.hasNext()) {
+                                builder.append("\n;");
+                                appendClause(clauseIterator.next(), builder);
+                        }
+                } else {
+                        builder.append("\n").append(INDENTATION).append("<no clauses>");
+                }
+                builder.append(".\n");
+                return builder.toString();
+        }
+
+        private static void appendClause(DnfClause clause, StringBuilder builder) {
+                var iterator = clause.literals().iterator();
+                if (!iterator.hasNext()) {
+                        builder.append("\n").append(INDENTATION).append("<empty>");
+                        return;
+                }
+                builder.append("\n").append(INDENTATION).append(iterator.next());
+                while (iterator.hasNext()) {
+                        builder.append(",\n").append(INDENTATION).append(iterator.next());
+                }
+        }
+
+        public static DnfBuilder builder() {
+                return builder(null);
+        }
+
+        public static DnfBuilder builder(String name) {
+                return new DnfBuilder(name);
+        }
+
+        public static Dnf of(Consumer<DnfBuilder> callback) {
+                return of(null, callback);
+        }
+
+        public static Dnf of(String name, Consumer<DnfBuilder> callback) {
+                var builder = builder(name);
+                callback.accept(builder);
+                return builder.build();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
new file mode 100644
index 00000000..8e38ca6b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
@@ -0,0 +1,262 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.dnf.callback.*;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.*;
+
+@SuppressWarnings("UnusedReturnValue")
+public final class DnfBuilder {
+        private final String name;
+        private final Set<Variable> parameterVariables = new LinkedHashSet<>();
+        private final List<SymbolicParameter> parameters = new ArrayList<>();
+        private final List<FunctionalDependency<Variable>> functionalDependencies = new ArrayList<>();
+        private final List<List<Literal>> clauses = new ArrayList<>();
+
+        DnfBuilder(String name) {
+                this.name = name;
+        }
+
+        public NodeVariable parameter() {
+                return parameter((String) null);
+        }
+
+        public NodeVariable parameter(String name) {
+                return parameter(name, ParameterDirection.OUT);
+        }
+
+        public NodeVariable parameter(ParameterDirection direction) {
+                return parameter((String) null, direction);
+        }
+
+        public NodeVariable parameter(String name, ParameterDirection direction) {
+                var variable = Variable.of(name);
+                parameter(variable, direction);
+                return variable;
+        }
+
+        public <T> DataVariable<T> parameter(Class<T> type) {
+                return parameter(null, type);
+        }
+
+        public <T> DataVariable<T> parameter(String name, Class<T> type) {
+                return parameter(name, type, ParameterDirection.OUT);
+        }
+
+        public <T> DataVariable<T> parameter(Class<T> type, ParameterDirection direction) {
+                return parameter(null, type, direction);
+        }
+
+        public <T> DataVariable<T> parameter(String name, Class<T> type, ParameterDirection direction) {
+                var variable = Variable.of(name, type);
+                parameter(variable, direction);
+                return variable;
+        }
+
+        public DnfBuilder parameter(Variable variable) {
+                return parameter(variable, ParameterDirection.OUT);
+        }
+
+        public DnfBuilder parameter(Variable variable, ParameterDirection direction) {
+                return symbolicParameter(new SymbolicParameter(variable, direction));
+        }
+
+        public DnfBuilder parameters(Variable... variables) {
+                return parameters(List.of(variables));
+        }
+
+        public DnfBuilder parameters(Collection<? extends Variable> variables) {
+                return parameters(variables, ParameterDirection.OUT);
+        }
+
+        public DnfBuilder parameters(Collection<? extends Variable> variables, ParameterDirection direction) {
+                for (var variable : variables) {
+                        parameter(variable, direction);
+                }
+                return this;
+        }
+
+        public DnfBuilder symbolicParameter(SymbolicParameter symbolicParameter) {
+                var variable = symbolicParameter.getVariable();
+                if (!parameterVariables.add(variable)) {
+                        throw new IllegalArgumentException("Variable %s is already on the parameter list %s"
+                                        .formatted(variable, parameters));
+                }
+                parameters.add(symbolicParameter);
+                return this;
+        }
+
+        public DnfBuilder symbolicParameters(SymbolicParameter... symbolicParameters) {
+                return symbolicParameters(List.of(symbolicParameters));
+        }
+
+        public DnfBuilder symbolicParameters(Collection<SymbolicParameter> symbolicParameters) {
+                for (var symbolicParameter : symbolicParameters) {
+                        symbolicParameter(symbolicParameter);
+                }
+                return this;
+        }
+
+        public DnfBuilder functionalDependencies(Collection<FunctionalDependency<Variable>> functionalDependencies) {
+                this.functionalDependencies.addAll(functionalDependencies);
+                return this;
+        }
+
+        public DnfBuilder functionalDependency(FunctionalDependency<Variable> functionalDependency) {
+                functionalDependencies.add(functionalDependency);
+                return this;
+        }
+
+        public DnfBuilder functionalDependency(Set<? extends Variable> forEach, Set<? extends Variable> unique) {
+                return functionalDependency(new FunctionalDependency<>(Set.copyOf(forEach), Set.copyOf(unique)));
+        }
+
+        public DnfBuilder clause(ClauseCallback0 callback) {
+                return clause(callback.toLiterals());
+        }
+
+        public DnfBuilder clause(ClauseCallback1Data0 callback) {
+                return clause(callback.toLiterals(Variable.of("v1")));
+        }
+
+        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback1Data1<T> callback) {
+                return clause(callback.toLiterals(Variable.of("v1", type1)));
+        }
+
+        public DnfBuilder clause(ClauseCallback2Data0 callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2")));
+        }
+
+        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback2Data1<T> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1)));
+        }
+
+        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback2Data2<T1, T2> callback) {
+                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2)));
+        }
+
+        public DnfBuilder clause(ClauseCallback3Data0 callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3")));
+        }
+
+        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback3Data1<T> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("d1", type1)));
+        }
+
+        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback3Data2<T1, T2> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1), Variable.of("d2", type2)));
+        }
+
+        public <T1, T2, T3> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3,
+                                                                                  ClauseCallback3Data3<T1, T2, T3> callback) {
+                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2),
+                                Variable.of("d3", type3)));
+        }
+
+        public DnfBuilder clause(ClauseCallback4Data0 callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3"), Variable.of("v4")));
+        }
+
+        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback4Data1<T> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3"), Variable.of("d1",
+                                type1)));
+        }
+
+        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback4Data2<T1, T2> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("d1", type1),
+                                Variable.of("d2", type2)));
+        }
+
+        public <T1, T2, T3> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3,
+                                                                                  ClauseCallback4Data3<T1, T2, T3> callback) {
+                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1), Variable.of("d2", type2),
+                                Variable.of("d3", type3)));
+        }
+
+        public <T1, T2, T3, T4> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3, Class<T4> type4,
+                                                                                          ClauseCallback4Data4<T1, T2, T3, T4> callback) {
+                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2),
+                                Variable.of("d3", type3), Variable.of("d4", type4)));
+        }
+
+        public DnfBuilder clause(Literal... literals) {
+                clause(List.of(literals));
+                return this;
+        }
+
+        public DnfBuilder clause(Collection<? extends Literal> literals) {
+                clauses.add(List.copyOf(literals));
+                return this;
+        }
+
+        <T> void output(DataVariable<T> outputVariable) {
+                // Copy parameter variables to exclude the newly added {@code outputVariable}.
+                var fromParameters = Set.copyOf(parameterVariables);
+                parameter(outputVariable, ParameterDirection.OUT);
+                functionalDependency(fromParameters, Set.of(outputVariable));
+        }
+
+        public Dnf build() {
+                var postProcessedClauses = postProcessClauses();
+                return new Dnf(name, Collections.unmodifiableList(parameters),
+                                Collections.unmodifiableList(functionalDependencies),
+                                Collections.unmodifiableList(postProcessedClauses));
+        }
+
+        private List<DnfClause> postProcessClauses() {
+                var parameterInfoMap = getParameterInfoMap();
+                var postProcessedClauses = new ArrayList<DnfClause>(clauses.size());
+                for (var literals : clauses) {
+                        var postProcessor = new ClausePostProcessor(parameterInfoMap, literals);
+                        var result = postProcessor.postProcessClause();
+                        if (result instanceof ClausePostProcessor.ClauseResult clauseResult) {
+                                postProcessedClauses.add(clauseResult.clause());
+                        } else if (result instanceof ClausePostProcessor.ConstantResult constantResult) {
+                                switch (constantResult) {
+                                case ALWAYS_TRUE -> {
+                                        var inputVariables = getInputVariables();
+                                        return List.of(new DnfClause(inputVariables, List.of()));
+                                }
+                                case ALWAYS_FALSE -> {
+                                        // Skip this clause because it can never match.
+                                }
+                                default -> throw new IllegalStateException("Unexpected ClausePostProcessor.ConstantResult: " +
+                                                constantResult);
+                                }
+                        } else {
+                                throw new IllegalStateException("Unexpected ClausePostProcessor.Result: " + result);
+                        }
+                }
+                return postProcessedClauses;
+        }
+
+        private Map<Variable, ClausePostProcessor.ParameterInfo> getParameterInfoMap() {
+                var mutableParameterInfoMap = new LinkedHashMap<Variable, ClausePostProcessor.ParameterInfo>();
+                int arity = parameters.size();
+                for (int i = 0; i < arity; i++) {
+                        var parameter = parameters.get(i);
+                        mutableParameterInfoMap.put(parameter.getVariable(),
+                                        new ClausePostProcessor.ParameterInfo(parameter.getDirection(), i));
+                }
+                return Collections.unmodifiableMap(mutableParameterInfoMap);
+        }
+
+        private Set<Variable> getInputVariables() {
+                var inputParameters = new LinkedHashSet<Variable>();
+                for (var parameter : parameters) {
+                        if (parameter.getDirection() == ParameterDirection.IN) {
+                                inputParameters.add(parameter.getVariable());
+                        }
+                }
+                return Collections.unmodifiableSet(inputParameters);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java
new file mode 100644
index 00000000..fdd0d47c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java
@@ -0,0 +1,28 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.List;
+import java.util.Set;
+
+public record DnfClause(Set<Variable> positiveVariables, List<Literal> literals) {
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, DnfClause other) {
+                int size = literals.size();
+                if (size != other.literals.size()) {
+                        return false;
+                }
+                for (int i = 0; i < size; i++) {
+                        if (!literals.get(i).equalsWithSubstitution(helper, other.literals.get(i))) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNFUtils.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfUtils.java
index 0ef77d49..65ab3634 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNFUtils.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfUtils.java
@@ -1,9 +1,14 @@
-package tools.refinery.store.query;
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
 
 import java.util.UUID;
 
-public final class DNFUtils {
-        private DNFUtils() {
+public final class DnfUtils {
+        private DnfUtils() {
                 throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
         }
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/FunctionalDependency.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalDependency.java
index 63a81713..b00b2cb7 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/FunctionalDependency.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalDependency.java
@@ -1,4 +1,9 @@
-package tools.refinery.store.query;
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
 
 import java.util.HashSet;
 import java.util.Set;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java
new file mode 100644
index 00000000..5a32b1ba
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java
@@ -0,0 +1,99 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.literal.CallPolarity;
+import tools.refinery.store.query.term.Aggregator;
+import tools.refinery.store.query.term.AssignedValue;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
+public final class FunctionalQuery<T> extends Query<T> {
+        private final Class<T> type;
+
+        FunctionalQuery(Dnf dnf, Class<T> type) {
+                super(dnf);
+                var parameters = dnf.getSymbolicParameters();
+                int outputIndex = dnf.arity() - 1;
+                for (int i = 0; i < outputIndex; i++) {
+                        var parameter = parameters.get(i);
+                        var parameterType = parameter.tryGetType();
+                        if (parameterType.isPresent()) {
+                                throw new IllegalArgumentException("Expected parameter %s of %s to be a node variable, got %s instead"
+                                                .formatted(parameter, dnf, parameterType.get().getName()));
+                        }
+                }
+                var outputParameter = parameters.get(outputIndex);
+                var outputParameterType = outputParameter.tryGetType();
+                if (outputParameterType.isEmpty() || !outputParameterType.get().equals(type)) {
+                        throw new IllegalArgumentException("Expected parameter %s of %s to be %s, but got %s instead".formatted(
+                                        outputParameter, dnf, type, outputParameterType.map(Class::getName).orElse("node")));
+                }
+                this.type = type;
+        }
+
+        @Override
+        public int arity() {
+                return getDnf().arity() - 1;
+        }
+
+        @Override
+        public Class<T> valueType() {
+                return type;
+        }
+
+        @Override
+        public T defaultValue() {
+                return null;
+        }
+
+        public AssignedValue<T> call(List<NodeVariable> arguments) {
+                return targetVariable -> {
+                        var argumentsWithTarget = new ArrayList<Variable>(arguments.size() + 1);
+                        argumentsWithTarget.addAll(arguments);
+                        argumentsWithTarget.add(targetVariable);
+                        return getDnf().call(CallPolarity.POSITIVE, argumentsWithTarget);
+                };
+        }
+
+        public AssignedValue<T> call(NodeVariable... arguments) {
+                return call(List.of(arguments));
+        }
+
+        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, List<NodeVariable> arguments) {
+                return targetVariable -> {
+                        var placeholderVariable = Variable.of(type);
+                        var argumentsWithPlaceholder = new ArrayList<Variable>(arguments.size() + 1);
+                        argumentsWithPlaceholder.addAll(arguments);
+                        argumentsWithPlaceholder.add(placeholderVariable);
+                        return getDnf()
+                                        .aggregateBy(placeholderVariable, aggregator, argumentsWithPlaceholder)
+                                        .toLiteral(targetVariable);
+                };
+        }
+
+        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, NodeVariable... arguments) {
+                return aggregate(aggregator, List.of(arguments));
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                FunctionalQuery<?> that = (FunctionalQuery<?>) o;
+                return Objects.equals(type, that.type);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), type);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java
new file mode 100644
index 00000000..d1cd7ba8
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.term.DataVariable;
+
+public final class FunctionalQueryBuilder<T> extends AbstractQueryBuilder<FunctionalQueryBuilder<T>> {
+        private final DataVariable<T> outputVariable;
+        private final Class<T> type;
+
+        FunctionalQueryBuilder(DataVariable<T> outputVariable, DnfBuilder dnfBuilder, Class<T> type) {
+                super(dnfBuilder);
+                this.outputVariable = outputVariable;
+                this.type = type;
+        }
+
+        @Override
+        protected FunctionalQueryBuilder<T> self() {
+                return this;
+        }
+
+        public FunctionalQuery<T> build() {
+                dnfBuilder.output(outputVariable);
+                return dnfBuilder.build().asFunction(type);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java
new file mode 100644
index 00000000..aaa52ce6
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java
@@ -0,0 +1,179 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.dnf.callback.*;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Objects;
+
+public abstract sealed class Query<T> implements AnyQuery permits FunctionalQuery, RelationalQuery {
+        private static final String OUTPUT_VARIABLE_NAME = "output";
+
+        private final Dnf dnf;
+
+        protected Query(Dnf dnf) {
+                for (var parameter : dnf.getSymbolicParameters()) {
+                        if (parameter.getDirection() != ParameterDirection.OUT) {
+                                throw new IllegalArgumentException("Query parameter %s with direction %s is not allowed"
+                                                .formatted(parameter.getVariable(), parameter.getDirection()));
+                        }
+                }
+                this.dnf = dnf;
+        }
+
+        @Override
+        public String name() {
+                return dnf.name();
+        }
+
+        @Override
+        public Dnf getDnf() {
+                return dnf;
+        }
+
+        // Allow redeclaration of the method with refined return type.
+        @SuppressWarnings("squid:S3038")
+        @Override
+        public abstract Class<T> valueType();
+
+        public abstract T defaultValue();
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Query<?> that = (Query<?>) o;
+                return Objects.equals(dnf, that.dnf);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(dnf);
+        }
+
+        @Override
+        public String toString() {
+                return dnf.toString();
+        }
+
+        public static QueryBuilder builder() {
+                return builder(null);
+        }
+
+        public static QueryBuilder builder(String name) {
+                return new QueryBuilder(name);
+        }
+
+        public static RelationalQuery of(QueryCallback0 callback) {
+                return of(null, callback);
+        }
+
+        public static RelationalQuery of(String name, QueryCallback0 callback) {
+                var builder = builder(name);
+                callback.accept(builder);
+                return builder.build();
+        }
+
+        public static RelationalQuery of(QueryCallback1 callback) {
+                return of(null, callback);
+        }
+
+        public static RelationalQuery of(String name, QueryCallback1 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"));
+                return builder.build();
+        }
+
+        public static RelationalQuery of(QueryCallback2 callback) {
+                return of(null, callback);
+        }
+
+        public static RelationalQuery of(String name, QueryCallback2 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"));
+                return builder.build();
+        }
+
+        public static RelationalQuery of(QueryCallback3 callback) {
+                return of(null, callback);
+        }
+
+        public static RelationalQuery of(String name, QueryCallback3 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"));
+                return builder.build();
+        }
+
+        public static RelationalQuery of(QueryCallback4 callback) {
+                return of(null, callback);
+        }
+
+        public static RelationalQuery of(String name, QueryCallback4 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
+                                builder.parameter("p4"));
+                return builder.build();
+        }
+
+        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback0<T> callback) {
+                return of(null, type, callback);
+        }
+
+        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback0<T> callback) {
+                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
+                var builder = builder(name).output(outputVariable);
+                callback.accept(builder, outputVariable);
+                return builder.build();
+        }
+
+        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback1<T> callback) {
+                return of(null, type, callback);
+        }
+
+        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback1<T> callback) {
+                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
+                var builder = builder(name).output(outputVariable);
+                callback.accept(builder, builder.parameter("p1"), outputVariable);
+                return builder.build();
+        }
+
+        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback2<T> callback) {
+                return of(null, type, callback);
+        }
+
+        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback2<T> callback) {
+                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
+                var builder = builder(name).output(outputVariable);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), outputVariable);
+                return builder.build();
+        }
+
+        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback3<T> callback) {
+                return of(null, type, callback);
+        }
+
+        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback3<T> callback) {
+                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
+                var builder = builder(name).output(outputVariable);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
+                                outputVariable);
+                return builder.build();
+        }
+
+        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback4<T> callback) {
+                return of(null, type, callback);
+        }
+
+        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback4<T> callback) {
+                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
+                var builder = builder(name).output(outputVariable);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
+                                builder.parameter("p4"), outputVariable);
+                return builder.build();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java
new file mode 100644
index 00000000..138911bc
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.term.DataVariable;
+
+public final class QueryBuilder extends AbstractQueryBuilder<QueryBuilder> {
+        QueryBuilder(String name) {
+                super(Dnf.builder(name));
+        }
+
+        @Override
+        protected QueryBuilder self() {
+                return this;
+        }
+
+        public <T> FunctionalQueryBuilder<T> output(DataVariable<T> outputVariable) {
+                return new FunctionalQueryBuilder<>(outputVariable, dnfBuilder, outputVariable.getType());
+        }
+
+        public RelationalQuery build() {
+                return dnfBuilder.build().asRelation();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java
new file mode 100644
index 00000000..d34a7ace
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java
@@ -0,0 +1,66 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.literal.CallLiteral;
+import tools.refinery.store.query.literal.CallPolarity;
+import tools.refinery.store.query.term.AssignedValue;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collections;
+import java.util.List;
+
+public final class RelationalQuery extends Query<Boolean> {
+        RelationalQuery(Dnf dnf) {
+                super(dnf);
+                for (var parameter : dnf.getSymbolicParameters()) {
+                        var parameterType = parameter.tryGetType();
+                        if (parameterType.isPresent()) {
+                                throw new IllegalArgumentException("Expected parameter %s of %s to be a node variable, got %s instead"
+                                                .formatted(parameter, dnf, parameterType.get().getName()));
+                        }
+                }
+        }
+
+        @Override
+        public int arity() {
+                return getDnf().arity();
+        }
+
+        @Override
+        public Class<Boolean> valueType() {
+                return Boolean.class;
+        }
+
+        @Override
+        public Boolean defaultValue() {
+                return false;
+        }
+
+        public CallLiteral call(CallPolarity polarity, List<NodeVariable> arguments) {
+                return getDnf().call(polarity, Collections.unmodifiableList(arguments));
+        }
+
+        public CallLiteral call(CallPolarity polarity, NodeVariable... arguments) {
+                return getDnf().call(polarity, arguments);
+        }
+
+        public CallLiteral call(NodeVariable... arguments) {
+                return getDnf().call(arguments);
+        }
+
+        public CallLiteral callTransitive(NodeVariable left, NodeVariable right) {
+                return getDnf().callTransitive(left, right);
+        }
+
+        public AssignedValue<Integer> count(List<NodeVariable> arguments) {
+                return getDnf().count(Collections.unmodifiableList(arguments));
+        }
+
+        public AssignedValue<Integer> count(NodeVariable... arguments) {
+                return getDnf().count(arguments);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java
new file mode 100644
index 00000000..e0d3ba1f
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java
@@ -0,0 +1,52 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Objects;
+
+public final class SymbolicParameter extends Parameter {
+        private final Variable variable;
+
+        public SymbolicParameter(Variable variable, ParameterDirection direction) {
+                super(variable.tryGetType().orElse(null), direction);
+                this.variable = variable;
+        }
+
+        public Variable getVariable() {
+                return variable;
+        }
+
+        public boolean isUnifiable() {
+                return variable.isUnifiable();
+        }
+
+        @Override
+        public String toString() {
+                var direction = getDirection();
+                if (direction == ParameterDirection.OUT) {
+                        return variable.toString();
+                }
+                return "%s %s".formatted(getDirection(), variable);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                SymbolicParameter that = (SymbolicParameter) o;
+                return Objects.equals(variable, that.variable);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), variable);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java
new file mode 100644
index 00000000..d98dda2e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback0 {
+        Collection<Literal> toLiterals();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java
new file mode 100644
index 00000000..4c01a527
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback1Data0 {
+        Collection<Literal> toLiterals(NodeVariable v1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java
new file mode 100644
index 00000000..2c0cb6eb
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback1Data1<T> {
+        Collection<Literal> toLiterals(DataVariable<T> d1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java
new file mode 100644
index 00000000..d764bdba
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback2Data0 {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java
new file mode 100644
index 00000000..140af03a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback2Data1<T> {
+        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T> x1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java
new file mode 100644
index 00000000..bfc8637c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback2Data2<T1, T2> {
+        Collection<Literal> toLiterals(DataVariable<T1> x1, DataVariable<T2> x2);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java
new file mode 100644
index 00000000..074df65b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback3Data0 {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java
new file mode 100644
index 00000000..24ba5187
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback3Data1<T> {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, DataVariable<T> d1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java
new file mode 100644
index 00000000..2a2e837a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback3Data2<T1, T2> {
+        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T1> d1, DataVariable<T2> d2);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java
new file mode 100644
index 00000000..8f4bdd01
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback3Data3<T1, T2, T3> {
+        Collection<Literal> toLiterals(DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java
new file mode 100644
index 00000000..ed0f87b2
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback4Data0 {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3, NodeVariable v4);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java
new file mode 100644
index 00000000..9b27e2e1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback4Data1<T> {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3, DataVariable<T> d1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java
new file mode 100644
index 00000000..cbc4808e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback4Data2<T1, T2> {
+        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, DataVariable<T1> d1, DataVariable<T2> d2);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java
new file mode 100644
index 00000000..a6258f36
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback4Data3<T1, T2, T3> {
+        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java
new file mode 100644
index 00000000..b52a911a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Collection;
+
+@FunctionalInterface
+public interface ClauseCallback4Data4<T1, T2, T3, T4> {
+        Collection<Literal> toLiterals(DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3, DataVariable<T4> d4);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java
new file mode 100644
index 00000000..63b3eee6
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
+import tools.refinery.store.query.term.DataVariable;
+
+@FunctionalInterface
+public interface FunctionalQueryCallback0<T> {
+        void accept(FunctionalQueryBuilder<T> builder, DataVariable<T> output);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java
new file mode 100644
index 00000000..1295a118
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface FunctionalQueryCallback1<T> {
+        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, DataVariable<T> output);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java
new file mode 100644
index 00000000..d5b7f9ff
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface FunctionalQueryCallback2<T> {
+        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, DataVariable<T> output);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java
new file mode 100644
index 00000000..dc8404a0
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface FunctionalQueryCallback3<T> {
+        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, NodeVariable p3,
+                                DataVariable<T> output);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java
new file mode 100644
index 00000000..b6d3ddb0
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface FunctionalQueryCallback4<T> {
+        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, NodeVariable p3, NodeVariable p4,
+                                DataVariable<T> output);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java
new file mode 100644
index 00000000..3cf1de48
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.QueryBuilder;
+
+@FunctionalInterface
+public interface QueryCallback0 {
+        void accept(QueryBuilder builder);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java
new file mode 100644
index 00000000..0a150955
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.QueryBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface QueryCallback1 {
+        void accept(QueryBuilder builder, NodeVariable p1);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java
new file mode 100644
index 00000000..9493a7b4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.QueryBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface QueryCallback2 {
+        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java
new file mode 100644
index 00000000..358c7da7
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.QueryBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface QueryCallback3 {
+        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java
new file mode 100644
index 00000000..890dda16
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf.callback;
+
+import tools.refinery.store.query.dnf.QueryBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+
+@FunctionalInterface
+public interface QueryCallback4 {
+        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3, NodeVariable p4);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java
new file mode 100644
index 00000000..1eeb5723
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java
@@ -0,0 +1,78 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.equality;
+
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.DnfClause;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.util.CycleDetectingMapper;
+
+import java.util.List;
+
+public class DeepDnfEqualityChecker implements DnfEqualityChecker {
+        private final CycleDetectingMapper<Pair, Boolean> mapper = new CycleDetectingMapper<>(Pair::toString,
+                        this::doCheckEqual);
+
+        @Override
+        public boolean dnfEqual(Dnf left, Dnf right) {
+                return mapper.map(new Pair(left, right));
+        }
+
+        public boolean dnfEqualRaw(List<SymbolicParameter> symbolicParameters,
+                                                           List<? extends List<? extends Literal>> clauses, Dnf other) {
+                int arity = symbolicParameters.size();
+                if (arity != other.arity()) {
+                        return false;
+                }
+                for (int i = 0; i < arity; i++) {
+                        if (!symbolicParameters.get(i).getDirection().equals(other.getSymbolicParameters().get(i).getDirection())) {
+                                return false;
+                        }
+                }
+                int numClauses = clauses.size();
+                if (numClauses != other.getClauses().size()) {
+                        return false;
+                }
+                for (int i = 0; i < numClauses; i++) {
+                        var literalEqualityHelper = new LiteralEqualityHelper(this, symbolicParameters,
+                                        other.getSymbolicParameters());
+                        if (!equalsWithSubstitutionRaw(literalEqualityHelper, clauses.get(i), other.getClauses().get(i))) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+
+        private boolean equalsWithSubstitutionRaw(LiteralEqualityHelper helper, List<? extends Literal> literals,
+                                                                                          DnfClause other) {
+                int size = literals.size();
+                if (size != other.literals().size()) {
+                        return false;
+                }
+                for (int i = 0; i < size; i++) {
+                        if (!literals.get(i).equalsWithSubstitution(helper, other.literals().get(i))) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+
+        protected boolean doCheckEqual(Pair pair) {
+                return pair.left.equalsWithSubstitution(this, pair.right);
+        }
+
+        protected List<Pair> getInProgress() {
+                return mapper.getInProgress();
+        }
+
+        protected record Pair(Dnf left, Dnf right) {
+                @Override
+                public String toString() {
+                        return "(%s, %s)".formatted(left.name(), right.name());
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java
new file mode 100644
index 00000000..4a8bee3b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.equality;
+
+import tools.refinery.store.query.dnf.Dnf;
+
+@FunctionalInterface
+public interface DnfEqualityChecker {
+        boolean dnfEqual(Dnf left, Dnf right);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java
new file mode 100644
index 00000000..9315fb30
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java
@@ -0,0 +1,54 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.equality;
+
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class LiteralEqualityHelper {
+        private final DnfEqualityChecker dnfEqualityChecker;
+        private final Map<Variable, Variable> leftToRight;
+        private final Map<Variable, Variable> rightToLeft;
+
+        public LiteralEqualityHelper(DnfEqualityChecker dnfEqualityChecker, List<SymbolicParameter> leftParameters,
+                                                                 List<SymbolicParameter> rightParameters) {
+                this.dnfEqualityChecker = dnfEqualityChecker;
+                var arity = leftParameters.size();
+                if (arity != rightParameters.size()) {
+                        throw new IllegalArgumentException("Parameter lists have unequal length");
+                }
+                leftToRight = new HashMap<>(arity);
+                rightToLeft = new HashMap<>(arity);
+                for (int i = 0; i < arity; i++) {
+                        if (!variableEqual(leftParameters.get(i).getVariable(), rightParameters.get(i).getVariable())) {
+                                throw new IllegalArgumentException("Parameter lists cannot be unified: duplicate parameter " + i);
+                        }
+                }
+        }
+
+        public boolean dnfEqual(Dnf left, Dnf right) {
+                return dnfEqualityChecker.dnfEqual(left, right);
+        }
+
+        public boolean variableEqual(Variable left, Variable right) {
+                if (checkMapping(leftToRight, left, right) && checkMapping(rightToLeft, right, left)) {
+                        leftToRight.put(left, right);
+                        rightToLeft.put(right, left);
+                        return true;
+                }
+                return false;
+        }
+
+        private static boolean checkMapping(Map<Variable, Variable> map, Variable key, Variable expectedValue) {
+                var currentValue = map.get(key);
+                return currentValue == null || currentValue.equals(expectedValue);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
new file mode 100644
index 00000000..8ef8e8b4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
@@ -0,0 +1,143 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.*;
+
+public abstract class AbstractCallLiteral implements Literal {
+        private final Constraint target;
+        private final List<Variable> arguments;
+        private final Set<Variable> inArguments;
+        private final Set<Variable> outArguments;
+
+        // Use exhaustive switch over enums.
+        @SuppressWarnings("squid:S1301")
+        protected AbstractCallLiteral(Constraint target, List<Variable> arguments) {
+                int arity = target.arity();
+                if (arguments.size() != arity) {
+                        throw new IllegalArgumentException("%s needs %d arguments, but got %s".formatted(target.name(),
+                                        target.arity(), arguments.size()));
+                }
+                this.target = target;
+                this.arguments = arguments;
+                var mutableInArguments = new LinkedHashSet<Variable>();
+                var mutableOutArguments = new LinkedHashSet<Variable>();
+                var parameters = target.getParameters();
+                for (int i = 0; i < arity; i++) {
+                        var argument = arguments.get(i);
+                        var parameter = parameters.get(i);
+                        if (!parameter.isAssignable(argument)) {
+                                throw new IllegalArgumentException("Argument %d of %s is not assignable to parameter %s"
+                                                .formatted(i, target, parameter));
+                        }
+                        switch (parameter.getDirection()) {
+                        case IN -> {
+                                if (mutableOutArguments.remove(argument)) {
+                                        checkInOutUnifiable(argument);
+                                }
+                                mutableInArguments.add(argument);
+                        }
+                        case OUT -> {
+                                if (mutableInArguments.contains(argument)) {
+                                        checkInOutUnifiable(argument);
+                                } else if (!mutableOutArguments.add(argument)) {
+                                        checkDuplicateOutUnifiable(argument);
+                                }
+                        }
+                        }
+                }
+                inArguments = Collections.unmodifiableSet(mutableInArguments);
+                outArguments = Collections.unmodifiableSet(mutableOutArguments);
+        }
+
+        private static void checkInOutUnifiable(Variable argument) {
+                if (!argument.isUnifiable()) {
+                        throw new IllegalArgumentException("Argument %s cannot appear with both %s and %s direction"
+                                        .formatted(argument, ParameterDirection.IN, ParameterDirection.OUT));
+                }
+        }
+
+        private static void checkDuplicateOutUnifiable(Variable argument) {
+                if (!argument.isUnifiable()) {
+                        throw new IllegalArgumentException("Argument %s cannot be bound multiple times".formatted(argument));
+                }
+        }
+
+        public Constraint getTarget() {
+                return target;
+        }
+
+        public List<Variable> getArguments() {
+                return arguments;
+        }
+
+        protected Set<Variable> getArgumentsOfDirection(ParameterDirection direction) {
+                return switch (direction) {
+                        case IN -> inArguments;
+                        case OUT -> outArguments;
+                };
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                var inputVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
+                inputVariables.retainAll(positiveVariablesInClause);
+                inputVariables.addAll(getArgumentsOfDirection(ParameterDirection.IN));
+                return Collections.unmodifiableSet(inputVariables);
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                var privateVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
+                privateVariables.removeAll(positiveVariablesInClause);
+                return Collections.unmodifiableSet(privateVariables);
+        }
+
+        @Override
+        public Literal substitute(Substitution substitution) {
+                var substitutedArguments = arguments.stream().map(substitution::getSubstitute).toList();
+                return doSubstitute(substitution, substitutedArguments);
+        }
+
+        protected abstract Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments);
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (other == null || getClass() != other.getClass()) {
+                        return false;
+                }
+                var otherCallLiteral = (AbstractCallLiteral) other;
+                var arity = arguments.size();
+                if (arity != otherCallLiteral.arguments.size()) {
+                        return false;
+                }
+                for (int i = 0; i < arity; i++) {
+                        if (!helper.variableEqual(arguments.get(i), otherCallLiteral.arguments.get(i))) {
+                                return false;
+                        }
+                }
+                return target.equals(helper, otherCallLiteral.target);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                AbstractCallLiteral that = (AbstractCallLiteral) o;
+                return target.equals(that.target) && arguments.equals(that.arguments);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), target, arguments);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
new file mode 100644
index 00000000..3a5eb5c7
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
@@ -0,0 +1,138 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.*;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+public class AggregationLiteral<R, T> extends AbstractCallLiteral {
+        private final DataVariable<R> resultVariable;
+        private final DataVariable<T> inputVariable;
+        private final Aggregator<R, T> aggregator;
+
+        public AggregationLiteral(DataVariable<R> resultVariable, Aggregator<R, T> aggregator,
+                                                          DataVariable<T> inputVariable, Constraint target, List<Variable> arguments) {
+                super(target, arguments);
+                if (!inputVariable.getType().equals(aggregator.getInputType())) {
+                        throw new IllegalArgumentException("Input variable %s must of type %s, got %s instead".formatted(
+                                        inputVariable, aggregator.getInputType().getName(), inputVariable.getType().getName()));
+                }
+                if (!getArgumentsOfDirection(ParameterDirection.OUT).contains(inputVariable)) {
+                        throw new IllegalArgumentException("Input variable %s must be bound with direction %s in the argument list"
+                                        .formatted(inputVariable, ParameterDirection.OUT));
+                }
+                if (!resultVariable.getType().equals(aggregator.getResultType())) {
+                        throw new IllegalArgumentException("Result variable %s must of type %s, got %s instead".formatted(
+                                        resultVariable, aggregator.getResultType().getName(), resultVariable.getType().getName()));
+                }
+                if (arguments.contains(resultVariable)) {
+                        throw new IllegalArgumentException("Result variable %s must not appear in the argument list".formatted(
+                                        resultVariable));
+                }
+                this.resultVariable = resultVariable;
+                this.inputVariable = inputVariable;
+                this.aggregator = aggregator;
+        }
+
+        public DataVariable<R> getResultVariable() {
+                return resultVariable;
+        }
+
+        public DataVariable<T> getInputVariable() {
+                return inputVariable;
+        }
+
+        public Aggregator<R, T> getAggregator() {
+                return aggregator;
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of(resultVariable);
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (positiveVariablesInClause.contains(inputVariable)) {
+                        throw new IllegalArgumentException("Aggregation variable %s must not be bound".formatted(inputVariable));
+                }
+                return super.getInputVariables(positiveVariablesInClause);
+        }
+
+        @Override
+        public Literal reduce() {
+                var reduction = getTarget().getReduction();
+                return switch (reduction) {
+                        case ALWAYS_FALSE -> {
+                                var emptyValue = aggregator.getEmptyResult();
+                                yield emptyValue == null ? BooleanLiteral.FALSE :
+                                                resultVariable.assign(new ConstantTerm<>(resultVariable.getType(), emptyValue));
+                        }
+                        case ALWAYS_TRUE -> throw new IllegalArgumentException("Trying to aggregate over an infinite set");
+                        case NOT_REDUCIBLE -> this;
+                };
+        }
+
+        @Override
+        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
+                return new AggregationLiteral<>(substitution.getTypeSafeSubstitute(resultVariable), aggregator,
+                                substitution.getTypeSafeSubstitute(inputVariable), getTarget(), substitutedArguments);
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherAggregationLiteral = (AggregationLiteral<?, ?>) other;
+                return helper.variableEqual(resultVariable, otherAggregationLiteral.resultVariable) &&
+                                aggregator.equals(otherAggregationLiteral.aggregator) &&
+                                helper.variableEqual(inputVariable, otherAggregationLiteral.inputVariable);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                AggregationLiteral<?, ?> that = (AggregationLiteral<?, ?>) o;
+                return resultVariable.equals(that.resultVariable) && inputVariable.equals(that.inputVariable) &&
+                                aggregator.equals(that.aggregator);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), resultVariable, inputVariable, aggregator);
+        }
+
+        @Override
+        public String toString() {
+                var builder = new StringBuilder();
+                builder.append(resultVariable);
+                builder.append(" is ");
+                builder.append(getTarget().toReferenceString());
+                builder.append("(");
+                var argumentIterator = getArguments().iterator();
+                if (argumentIterator.hasNext()) {
+                        var argument = argumentIterator.next();
+                        if (inputVariable.equals(argument)) {
+                                builder.append("@Aggregate(\"").append(aggregator).append("\") ");
+                        }
+                        builder.append(argument);
+                        while (argumentIterator.hasNext()) {
+                                builder.append(", ").append(argumentIterator.next());
+                        }
+                }
+                builder.append(")");
+                return builder.toString();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java
new file mode 100644
index 00000000..dbf999a2
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java
@@ -0,0 +1,79 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Collections;
+import java.util.Objects;
+import java.util.Set;
+
+public record AssignLiteral<T>(DataVariable<T> variable, Term<T> term) implements Literal {
+        public AssignLiteral {
+                if (!term.getType().equals(variable.getType())) {
+                        throw new IllegalArgumentException("Term %s must be of type %s, got %s instead".formatted(
+                                        term, variable.getType().getName(), term.getType().getName()));
+                }
+                var inputVariables = term.getInputVariables();
+                if (inputVariables.contains(variable)) {
+                        throw new IllegalArgumentException("Result variable %s must not appear in the term %s".formatted(
+                                        variable, term));
+                }
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of(variable);
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Collections.unmodifiableSet(term.getInputVariables());
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public Literal substitute(Substitution substitution) {
+                return new AssignLiteral<>(substitution.getTypeSafeSubstitute(variable), term.substitute(substitution));
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (other == null || getClass() != other.getClass()) {
+                        return false;
+                }
+                var otherLetLiteral = (AssignLiteral<?>) other;
+                return helper.variableEqual(variable, otherLetLiteral.variable) && term.equalsWithSubstitution(helper,
+                                otherLetLiteral.term);
+        }
+
+        @Override
+        public String toString() {
+                return "%s is (%s)".formatted(variable, term);
+        }
+
+        @Override
+        public boolean equals(Object obj) {
+                if (obj == this) return true;
+                if (obj == null || obj.getClass() != this.getClass()) return false;
+                var that = (AssignLiteral<?>) obj;
+                return Objects.equals(this.variable, that.variable) &&
+                                Objects.equals(this.term, that.term);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), variable, term);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssumeLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssumeLiteral.java
new file mode 100644
index 00000000..1ca04c77
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssumeLiteral.java
@@ -0,0 +1,83 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Collections;
+import java.util.Objects;
+import java.util.Set;
+
+public record AssumeLiteral(Term<Boolean> term) implements Literal {
+        public AssumeLiteral {
+                if (!term.getType().equals(Boolean.class)) {
+                        throw new IllegalArgumentException("Term %s must be of type %s, got %s instead".formatted(
+                                        term, Boolean.class.getName(), term.getType().getName()));
+                }
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of();
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Collections.unmodifiableSet(term.getInputVariables());
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+
+        @Override
+        public Literal substitute(Substitution substitution) {
+                return new AssumeLiteral(term.substitute(substitution));
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (other == null || getClass() != other.getClass()) {
+                        return false;
+                }
+                var otherAssumeLiteral = (AssumeLiteral) other;
+                return term.equalsWithSubstitution(helper, otherAssumeLiteral.term);
+        }
+
+        @Override
+        public Literal reduce() {
+                if (term instanceof ConstantTerm<Boolean> constantTerm) {
+                        // Return {@link BooleanLiteral#FALSE} for {@code false} or {@code null} literals.
+                        return Boolean.TRUE.equals(constantTerm.getValue()) ? BooleanLiteral.TRUE :
+                                        BooleanLiteral.FALSE;
+                }
+                return this;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s)".formatted(term);
+        }
+
+        @Override
+        public boolean equals(Object obj) {
+                if (obj == this) return true;
+                if (obj == null || obj.getClass() != this.getClass()) return false;
+                var that = (AssumeLiteral) obj;
+                return Objects.equals(this.term, that.term);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), term);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java
new file mode 100644
index 00000000..f312d202
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java
@@ -0,0 +1,63 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Set;
+
+public enum BooleanLiteral implements CanNegate<BooleanLiteral> {
+        TRUE(true),
+        FALSE(false);
+
+        private final boolean value;
+
+        BooleanLiteral(boolean value) {
+                this.value = value;
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of();
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public Literal substitute(Substitution substitution) {
+                // No variables to substitute.
+                return this;
+        }
+
+        @Override
+        public BooleanLiteral negate() {
+                return fromBoolean(!value);
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                return equals(other);
+        }
+
+        @Override
+        public String toString() {
+                return Boolean.toString(value);
+        }
+
+        public static BooleanLiteral fromBoolean(boolean value) {
+                return value ? TRUE : FALSE;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
new file mode 100644
index 00000000..29772aee
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
@@ -0,0 +1,130 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.*;
+
+public final class CallLiteral extends AbstractCallLiteral implements CanNegate<CallLiteral> {
+        private final CallPolarity polarity;
+
+        public CallLiteral(CallPolarity polarity, Constraint target, List<Variable> arguments) {
+                super(target, arguments);
+                var parameters = target.getParameters();
+                int arity = target.arity();
+                if (polarity.isTransitive()) {
+                        if (arity != 2) {
+                                throw new IllegalArgumentException("Transitive closures can only take binary relations");
+                        }
+                        if (parameters.get(0).isDataVariable() || parameters.get(1).isDataVariable()) {
+                                throw new IllegalArgumentException("Transitive closures can only be computed over nodes");
+                        }
+                }
+                this.polarity = polarity;
+        }
+
+        public CallPolarity getPolarity() {
+                return polarity;
+        }
+
+        @Override
+        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
+                return new CallLiteral(polarity, getTarget(), substitutedArguments);
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                if (polarity.isPositive()) {
+                        return getArgumentsOfDirection(ParameterDirection.OUT);
+                }
+                return Set.of();
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (polarity.isPositive()) {
+                        return getArgumentsOfDirection(ParameterDirection.IN);
+                }
+                return super.getInputVariables(positiveVariablesInClause);
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (polarity.isPositive()) {
+                        return Set.of();
+                }
+                return super.getPrivateVariables(positiveVariablesInClause);
+        }
+
+        @Override
+        public Literal reduce() {
+                var reduction = getTarget().getReduction();
+                var negatedReduction = polarity.isPositive() ? reduction : reduction.negate();
+                return switch (negatedReduction) {
+                        case ALWAYS_TRUE -> BooleanLiteral.TRUE;
+                        case ALWAYS_FALSE -> BooleanLiteral.FALSE;
+                        default -> this;
+                };
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherCallLiteral = (CallLiteral) other;
+                return polarity.equals(otherCallLiteral.polarity);
+        }
+
+        @Override
+        public CallLiteral negate() {
+                return new CallLiteral(polarity.negate(), getTarget(), getArguments());
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                CallLiteral that = (CallLiteral) o;
+                return polarity == that.polarity;
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), polarity);
+        }
+
+        @Override
+        public String toString() {
+                var builder = new StringBuilder();
+                if (!polarity.isPositive()) {
+                        builder.append("!(");
+                }
+                builder.append(getTarget().toReferenceString());
+                if (polarity.isTransitive()) {
+                        builder.append("+");
+                }
+                builder.append("(");
+                var argumentIterator = getArguments().iterator();
+                if (argumentIterator.hasNext()) {
+                        builder.append(argumentIterator.next());
+                        while (argumentIterator.hasNext()) {
+                                builder.append(", ").append(argumentIterator.next());
+                        }
+                }
+                builder.append(")");
+                if (!polarity.isPositive()) {
+                        builder.append(")");
+                }
+                return builder.toString();
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallPolarity.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
index 957e9b7b..ca70b0fd 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallPolarity.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
@@ -1,4 +1,9 @@
-package tools.refinery.store.query.atom;
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
 
 public enum CallPolarity {
         POSITIVE(true, false),
@@ -22,7 +27,11 @@ public enum CallPolarity {
                 return transitive;
         }
 
-        public static CallPolarity fromBoolean(boolean positive) {
-                return positive ? POSITIVE : NEGATIVE;
+        public CallPolarity negate() {
+                return switch (this) {
+                        case POSITIVE -> NEGATIVE;
+                        case NEGATIVE -> POSITIVE;
+                        case TRANSITIVE -> throw new IllegalArgumentException("Transitive polarity cannot be negated");
+                };
         }
 }
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java
new file mode 100644
index 00000000..35dcb3fb
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java
@@ -0,0 +1,10 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+public interface CanNegate<T extends CanNegate<T>> extends Literal {
+        T negate();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
new file mode 100644
index 00000000..73545620
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Objects;
+import java.util.Set;
+
+public record ConstantLiteral(NodeVariable variable, int nodeId) implements Literal {
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of(variable);
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public ConstantLiteral substitute(Substitution substitution) {
+                return new ConstantLiteral(substitution.getTypeSafeSubstitute(variable), nodeId);
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (other.getClass() != getClass()) {
+                        return false;
+                }
+                var otherConstantLiteral = (ConstantLiteral) other;
+                return helper.variableEqual(variable, otherConstantLiteral.variable) && nodeId == otherConstantLiteral.nodeId;
+        }
+
+
+        @Override
+        public String toString() {
+                return "%s === @Constant %d".formatted(variable, nodeId);
+        }
+
+        @Override
+        public boolean equals(Object obj) {
+                if (obj == this) return true;
+                if (obj == null || obj.getClass() != this.getClass()) return false;
+                var that = (ConstantLiteral) obj;
+                return Objects.equals(this.variable, that.variable) &&
+                                this.nodeId == that.nodeId;
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), variable, nodeId);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java
new file mode 100644
index 00000000..4d4749c8
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java
@@ -0,0 +1,101 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.term.int_.IntTerms;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+public class CountLiteral extends AbstractCallLiteral {
+        private final DataVariable<Integer> resultVariable;
+
+        public CountLiteral(DataVariable<Integer> resultVariable, Constraint target, List<Variable> arguments) {
+                super(target, arguments);
+                if (!resultVariable.getType().equals(Integer.class)) {
+                        throw new IllegalArgumentException("Count result variable %s must be of type %s, got %s instead".formatted(
+                                        resultVariable, Integer.class.getName(), resultVariable.getType().getName()));
+                }
+                if (arguments.contains(resultVariable)) {
+                        throw new IllegalArgumentException("Count result variable %s must not appear in the argument list"
+                                        .formatted(resultVariable));
+                }
+                this.resultVariable = resultVariable;
+        }
+
+        public DataVariable<Integer> getResultVariable() {
+                return resultVariable;
+        }
+
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of(resultVariable);
+        }
+
+        @Override
+        public Literal reduce() {
+                var reduction = getTarget().getReduction();
+                return switch (reduction) {
+                        case ALWAYS_FALSE -> getResultVariable().assign(IntTerms.constant(0));
+                        // The only way a constant {@code true} predicate can be called in a negative position is to have all of
+                        // its arguments bound as input variables. Thus, there will only be a single match.
+                        case ALWAYS_TRUE -> getResultVariable().assign(IntTerms.constant(1));
+                        case NOT_REDUCIBLE -> this;
+                };
+        }
+
+        @Override
+        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
+                return new CountLiteral(substitution.getTypeSafeSubstitute(resultVariable), getTarget(), substitutedArguments);
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherCountLiteral = (CountLiteral) other;
+                return helper.variableEqual(resultVariable, otherCountLiteral.resultVariable);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                CountLiteral that = (CountLiteral) o;
+                return resultVariable.equals(that.resultVariable);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), resultVariable);
+        }
+
+        @Override
+        public String toString() {
+                var builder = new StringBuilder();
+                builder.append(resultVariable);
+                builder.append(" is count ");
+                builder.append(getTarget().toReferenceString());
+                builder.append("(");
+                var argumentIterator = getArguments().iterator();
+                if (argumentIterator.hasNext()) {
+                        builder.append(argumentIterator.next());
+                        while (argumentIterator.hasNext()) {
+                                builder.append(", ").append(argumentIterator.next());
+                        }
+                }
+                builder.append(")");
+                return builder.toString();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
new file mode 100644
index 00000000..28ba7625
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
@@ -0,0 +1,81 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Objects;
+import java.util.Set;
+
+public record EquivalenceLiteral(boolean positive, NodeVariable left, NodeVariable right)
+                implements CanNegate<EquivalenceLiteral> {
+        @Override
+        public Set<Variable> getOutputVariables() {
+                return Set.of(left);
+        }
+
+        @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of(right);
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                return Set.of();
+        }
+
+        @Override
+        public EquivalenceLiteral negate() {
+                return new EquivalenceLiteral(!positive, left, right);
+        }
+
+        @Override
+        public EquivalenceLiteral substitute(Substitution substitution) {
+                return new EquivalenceLiteral(positive, substitution.getTypeSafeSubstitute(left),
+                                substitution.getTypeSafeSubstitute(right));
+        }
+
+        @Override
+        public Literal reduce() {
+                if (left.equals(right)) {
+                        return positive ? BooleanLiteral.TRUE : BooleanLiteral.FALSE;
+                }
+                return this;
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
+                if (other.getClass() != getClass()) {
+                        return false;
+                }
+                var otherEquivalenceLiteral = (EquivalenceLiteral) other;
+                return helper.variableEqual(left, otherEquivalenceLiteral.left) && helper.variableEqual(right,
+                                otherEquivalenceLiteral.right);
+        }
+
+        @Override
+        public String toString() {
+                return "%s %s %s".formatted(left, positive ? "===" : "!==", right);
+        }
+
+        @Override
+        public boolean equals(Object obj) {
+                if (obj == this) return true;
+                if (obj == null || obj.getClass() != this.getClass()) return false;
+                var that = (EquivalenceLiteral) obj;
+                return this.positive == that.positive &&
+                                Objects.equals(this.left, that.left) &&
+                                Objects.equals(this.right, that.right);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), positive, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java
new file mode 100644
index 00000000..ce6c11fe
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Set;
+
+public interface Literal {
+        Set<Variable> getOutputVariables();
+
+        Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause);
+
+        Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause);
+
+        Literal substitute(Substitution substitution);
+
+        default Literal reduce() {
+                return this;
+        }
+
+        @SuppressWarnings("BooleanMethodIsAlwaysInverted")
+        boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java
new file mode 100644
index 00000000..b3a87811
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import tools.refinery.store.query.term.Term;
+
+public final class Literals {
+        private Literals() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static <T extends CanNegate<T>> T not(CanNegate<T> literal) {
+                return literal.negate();
+        }
+
+        public static AssumeLiteral assume(Term<Boolean> term) {
+                return new AssumeLiteral(term);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java
new file mode 100644
index 00000000..ee155a9a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+public enum Reduction {
+        /**
+         * Signifies that a literal should be preserved in the clause.
+         */
+        NOT_REDUCIBLE,
+
+        /**
+         * Signifies that the literal may be omitted from the cause (if the model being queried is nonempty).
+         */
+        ALWAYS_TRUE,
+
+        /**
+         * Signifies that the clause with the literal may be omitted entirely.
+         */
+        ALWAYS_FALSE;
+
+        public Reduction negate() {
+                return switch (this) {
+                        case NOT_REDUCIBLE -> NOT_REDUCIBLE;
+                        case ALWAYS_TRUE -> ALWAYS_FALSE;
+                        case ALWAYS_FALSE -> ALWAYS_TRUE;
+                };
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java
new file mode 100644
index 00000000..a710c64d
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java
@@ -0,0 +1,63 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public abstract class AbstractResultSet<T> implements ResultSet<T> {
+        private final ModelQueryAdapter adapter;
+        private final Query<T> query;
+        private final List<ResultSetListener<T>> listeners = new ArrayList<>();
+
+        protected AbstractResultSet(ModelQueryAdapter adapter, Query<T> query) {
+                this.adapter = adapter;
+                this.query = query;
+        }
+
+        @Override
+        public ModelQueryAdapter getAdapter() {
+                return adapter;
+        }
+
+        @Override
+        public Query<T> getQuery() {
+                return query;
+        }
+
+        @Override
+        public void addListener(ResultSetListener<T> listener) {
+                if (listeners.isEmpty()) {
+                        startListeningForChanges();
+                }
+                listeners.add(listener);
+        }
+
+        @Override
+        public void removeListener(ResultSetListener<T> listener) {
+                listeners.remove(listener);
+                if (listeners.isEmpty()) {
+                        stopListeningForChanges();
+                }
+        }
+
+        protected abstract void startListeningForChanges();
+
+        protected abstract void stopListeningForChanges();
+
+        protected void notifyChange(Tuple key, T oldValue, T newValue) {
+                int listenerCount = listeners.size();
+                // Use a for loop instead of a for-each loop to avoid {@code Iterator} allocation overhead.
+                //noinspection ForLoopReplaceableByForEach
+                for (int i = 0; i < listenerCount; i++) {
+                        listeners.get(i).put(key, oldValue, newValue);
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java
new file mode 100644
index 00000000..02809477
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.AnyQuery;
+
+public sealed interface AnyResultSet permits ResultSet {
+        ModelQueryAdapter getAdapter();
+
+        AnyQuery getQuery();
+
+        int size();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java
new file mode 100644
index 00000000..2795a44b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java
@@ -0,0 +1,49 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.map.Cursors;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.tuple.Tuple;
+
+public record EmptyResultSet<T>(ModelQueryAdapter adapter, Query<T> query) implements ResultSet<T> {
+        @Override
+        public ModelQueryAdapter getAdapter() {
+                return adapter;
+        }
+
+        @Override
+        public Query<T> getQuery() {
+                return query;
+        }
+
+        @Override
+        public T get(Tuple parameters) {
+                return query.defaultValue();
+        }
+
+        @Override
+        public Cursor<Tuple, T> getAll() {
+                return Cursors.empty();
+        }
+
+        @Override
+        public int size() {
+                return 0;
+        }
+
+        @Override
+        public void addListener(ResultSetListener<T> listener) {
+                // No need to store the listener, because the empty result set will never change.
+        }
+
+        @Override
+        public void removeListener(ResultSetListener<T> listener) {
+                // No need to remove the listener, because we never stored it.
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java
new file mode 100644
index 00000000..39006d65
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java
@@ -0,0 +1,80 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.query.utils.OrderStatisticTree;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Objects;
+
+public class OrderedResultSet<T> implements AutoCloseable, ResultSet<T> {
+        private final ResultSet<T> resultSet;
+        private final OrderStatisticTree<Tuple> tree = new OrderStatisticTree<>();
+        private final ResultSetListener<T> listener = (key, fromValue, toValue) -> {
+                var defaultValue = getQuery().defaultValue();
+                if (Objects.equals(defaultValue, toValue)) {
+                        tree.remove(key);
+                } else {
+                        tree.add(key);
+                }
+        };
+
+        public OrderedResultSet(ResultSet<T> resultSet) {
+                this.resultSet = resultSet;
+                resultSet.addListener(listener);
+                var cursor = resultSet.getAll();
+                while (cursor.move()) {
+                        tree.add(cursor.getKey());
+                }
+        }
+
+        @Override
+        public ModelQueryAdapter getAdapter() {
+                return resultSet.getAdapter();
+        }
+
+        @Override
+        public int size() {
+                return resultSet.size();
+        }
+
+        @Override
+        public Query<T> getQuery() {
+                return resultSet.getQuery();
+        }
+
+        @Override
+        public T get(Tuple parameters) {
+                return resultSet.get(parameters);
+        }
+
+        public Tuple getKey(int index) {
+                return tree.get(index);
+        }
+
+        @Override
+        public Cursor<Tuple, T> getAll() {
+                return resultSet.getAll();
+        }
+
+        @Override
+        public void addListener(ResultSetListener<T> listener) {
+                resultSet.addListener(listener);
+        }
+
+        @Override
+        public void removeListener(ResultSetListener<T> listener) {
+                resultSet.removeListener(listener);
+        }
+
+        @Override
+        public void close() {
+                resultSet.removeListener(listener);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java
new file mode 100644
index 00000000..33d1ea95
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.query.dnf.Query;
+import tools.refinery.store.tuple.Tuple;
+
+public non-sealed interface ResultSet<T> extends AnyResultSet {
+        Query<T> getQuery();
+
+        T get(Tuple parameters);
+
+        Cursor<Tuple, T> getAll();
+
+        void addListener(ResultSetListener<T> listener);
+
+        void removeListener(ResultSetListener<T> listener);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSetListener.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSetListener.java
new file mode 100644
index 00000000..fd8a503e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSetListener.java
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.resultset;
+
+import tools.refinery.store.tuple.Tuple;
+
+@FunctionalInterface
+public interface ResultSetListener<T> {
+        void put(Tuple key, T fromValue, T toValue);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java
new file mode 100644
index 00000000..a8201eef
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java
@@ -0,0 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.substitution;
+
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Map;
+
+public record MapBasedSubstitution(Map<Variable, Variable> map, Substitution fallback) implements Substitution {
+        @Override
+        public Variable getSubstitute(Variable variable) {
+                var value = map.get(variable);
+                return value == null ? fallback.getSubstitute(variable) : value;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java
new file mode 100644
index 00000000..9b737ceb
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java
@@ -0,0 +1,20 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.substitution;
+
+import tools.refinery.store.query.term.Variable;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class RenewingSubstitution implements Substitution {
+        private final Map<Variable, Variable> alreadyRenewed = new HashMap<>();
+
+        @Override
+        public Variable getSubstitute(Variable variable) {
+                return alreadyRenewed.computeIfAbsent(variable, Variable::renew);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java
new file mode 100644
index 00000000..bb3803d3
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java
@@ -0,0 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.substitution;
+
+import tools.refinery.store.query.term.Variable;
+
+public enum StatelessSubstitution implements Substitution {
+        FAILING {
+                @Override
+                public Variable getSubstitute(Variable variable) {
+                        throw new IllegalArgumentException("No substitute for " + variable);
+                }
+        },
+        IDENTITY {
+                @Override
+                public Variable getSubstitute(Variable variable) {
+                        return variable;
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java
new file mode 100644
index 00000000..834fce12
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.substitution;
+
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+
+@FunctionalInterface
+public interface Substitution {
+        Variable getSubstitute(Variable variable);
+
+        default NodeVariable getTypeSafeSubstitute(NodeVariable variable) {
+                var substitute = getSubstitute(variable);
+                return substitute.asNodeVariable();
+        }
+
+        default <T> DataVariable<T> getTypeSafeSubstitute(DataVariable<T> variable) {
+                var substitute = getSubstitute(variable);
+                return substitute.asDataVariable(variable.getType());
+        }
+
+        static SubstitutionBuilder builder() {
+                return new SubstitutionBuilder();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java
new file mode 100644
index 00000000..37fb6908
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java
@@ -0,0 +1,79 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.substitution;
+
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@SuppressWarnings("UnusedReturnValue")
+public class SubstitutionBuilder {
+        private final Map<Variable, Variable> map = new HashMap<>();
+        private Substitution fallback;
+
+        SubstitutionBuilder() {
+                total();
+        }
+
+        public SubstitutionBuilder put(NodeVariable original, NodeVariable substitute) {
+                return putChecked(original, substitute);
+        }
+
+        public <T> SubstitutionBuilder put(DataVariable<T> original, DataVariable<T> substitute) {
+                return putChecked(original, substitute);
+        }
+
+        public SubstitutionBuilder putChecked(Variable original, Variable substitute) {
+                if (!original.tryGetType().equals(substitute.tryGetType())) {
+                        throw new IllegalArgumentException("Cannot substitute variable %s of sort %s with variable %s of sort %s"
+                                        .formatted(original, original.tryGetType().map(Class::getName).orElse("node"), substitute,
+                                                        substitute.tryGetType().map(Class::getName).orElse("node")));
+                }
+                if (map.containsKey(original)) {
+                        throw new IllegalArgumentException("Already has substitution for variable %s".formatted(original));
+                }
+                map.put(original, substitute);
+                return this;
+        }
+
+        public SubstitutionBuilder putManyChecked(List<Variable> originals, List<Variable> substitutes) {
+                int size = originals.size();
+                if (size != substitutes.size()) {
+                        throw new IllegalArgumentException("Cannot substitute %d variables %s with %d variables %s"
+                                        .formatted(size, originals, substitutes.size(), substitutes));
+                }
+                for (int i = 0; i < size; i++) {
+                        putChecked(originals.get(i), substitutes.get(i));
+                }
+                return this;
+        }
+
+        public SubstitutionBuilder fallback(Substitution newFallback) {
+                fallback = newFallback;
+                return this;
+        }
+
+        public SubstitutionBuilder total() {
+                return fallback(StatelessSubstitution.FAILING);
+        }
+
+        public SubstitutionBuilder partial() {
+                return fallback(StatelessSubstitution.IDENTITY);
+        }
+
+        public SubstitutionBuilder renewing() {
+                return fallback(new RenewingSubstitution());
+        }
+
+        public Substitution build() {
+                return map.isEmpty() ? fallback : new MapBasedSubstitution(Collections.unmodifiableMap(map), fallback);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java
new file mode 100644
index 00000000..d0ae3c12
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java
@@ -0,0 +1,41 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+
+import java.util.Objects;
+
+public abstract class AbstractTerm<T> implements Term<T> {
+        private final Class<T> type;
+
+        protected AbstractTerm(Class<T> type) {
+                this.type = type;
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                return getClass().equals(other.getClass()) && type.equals(other.getType());
+        }
+
+        @Override
+        public Class<T> getType() {
+                return type;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                AbstractTerm<?> that = (AbstractTerm<?>) o;
+                return type.equals(that.type);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), type);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java
new file mode 100644
index 00000000..0684a9d9
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java
@@ -0,0 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import java.util.stream.Stream;
+
+public interface Aggregator<R, T> {
+        Class<R> getResultType();
+
+        Class<T> getInputType();
+
+        R aggregateStream(Stream<T> stream);
+
+        R getEmptyResult();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java
new file mode 100644
index 00000000..192c39c5
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java
@@ -0,0 +1,49 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+
+import java.util.Optional;
+import java.util.Set;
+
+public abstract sealed class AnyDataVariable extends Variable implements AnyTerm permits DataVariable {
+        protected AnyDataVariable(String name) {
+                super(name);
+        }
+
+        @Override
+        public Optional<Class<?>> tryGetType() {
+                return Optional.of(getType());
+        }
+
+        @Override
+        public NodeVariable asNodeVariable() {
+                throw new IllegalStateException("%s is a data variable".formatted(this));
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                return other instanceof AnyDataVariable dataVariable && helper.variableEqual(this, dataVariable);
+        }
+
+        @Override
+        public Set<AnyDataVariable> getInputVariables() {
+                return Set.of(this);
+        }
+
+        @Override
+        public boolean isUnifiable() {
+                return false;
+        }
+
+        @Override
+        public abstract AnyDataVariable renew(@Nullable String name);
+
+        @Override
+        public abstract AnyDataVariable renew();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java
new file mode 100644
index 00000000..c12c0166
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+
+import java.util.Set;
+
+public sealed interface AnyTerm permits AnyDataVariable, Term {
+        Class<?> getType();
+
+        AnyTerm substitute(Substitution substitution);
+
+        boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other);
+
+        Set<AnyDataVariable> getInputVariables();
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java
new file mode 100644
index 00000000..0cf30aa6
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.literal.Literal;
+
+@FunctionalInterface
+public interface AssignedValue<T> {
+        Literal toLiteral(DataVariable<T> targetVariable);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java
new file mode 100644
index 00000000..8ad17839
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java
@@ -0,0 +1,113 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.valuation.Valuation;
+
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Objects;
+import java.util.Set;
+
+public abstract class BinaryTerm<R, T1, T2> extends AbstractTerm<R> {
+        private final Class<T1> leftType;
+        private final Class<T2> rightType;
+        private final Term<T1> left;
+        private final Term<T2> right;
+
+        protected BinaryTerm(Class<R> type, Class<T1> leftType, Class<T2> rightType, Term<T1> left, Term<T2> right) {
+                super(type);
+                if (!left.getType().equals(leftType)) {
+                        throw new IllegalArgumentException("Expected left %s to be of type %s, got %s instead".formatted(
+                                        left, leftType.getName(), left.getType().getName()));
+                }
+                if (!right.getType().equals(rightType)) {
+                        throw new IllegalArgumentException("Expected right %s to be of type %s, got %s instead".formatted(
+                                        right, rightType.getName(), right.getType().getName()));
+                }
+                this.leftType = leftType;
+                this.rightType = rightType;
+                this.left = left;
+                this.right = right;
+        }
+
+        public Class<T1> getLeftType() {
+                return leftType;
+        }
+
+        public Class<T2> getRightType() {
+                return rightType;
+        }
+
+        public Term<T1> getLeft() {
+                return left;
+        }
+
+        public Term<T2> getRight() {
+                return right;
+        }
+
+        @Override
+        public R evaluate(Valuation valuation) {
+                var leftValue = left.evaluate(valuation);
+                if (leftValue == null) {
+                        return null;
+                }
+                var rightValue = right.evaluate(valuation);
+                if (rightValue == null) {
+                        return null;
+                }
+                return doEvaluate(leftValue, rightValue);
+        }
+
+        protected abstract R doEvaluate(T1 leftValue, T2 rightValue);
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherBinaryTerm = (BinaryTerm<?, ?, ?>) other;
+                return leftType.equals(otherBinaryTerm.leftType) &&
+                                rightType.equals(otherBinaryTerm.rightType) &&
+                                left.equalsWithSubstitution(helper, otherBinaryTerm.left) &&
+                                right.equalsWithSubstitution(helper, otherBinaryTerm.right);
+        }
+
+        @Override
+        public Term<R> substitute(Substitution substitution) {
+                return doSubstitute(substitution, left.substitute(substitution), right.substitute(substitution));
+        }
+
+        public abstract Term<R> doSubstitute(Substitution substitution, Term<T1> substitutedLeft,
+                                                                                 Term<T2> substitutedRight);
+
+        @Override
+        public Set<AnyDataVariable> getInputVariables() {
+                var inputVariables = new HashSet<>(left.getInputVariables());
+                inputVariables.addAll(right.getInputVariables());
+                return Collections.unmodifiableSet(inputVariables);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                BinaryTerm<?, ?, ?> that = (BinaryTerm<?, ?, ?>) o;
+                return Objects.equals(leftType, that.leftType) &&
+                                Objects.equals(rightType, that.rightType) &&
+                                Objects.equals(left, that.left) &&
+                                Objects.equals(right, that.right);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), leftType, rightType, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java
new file mode 100644
index 00000000..2f6c56d1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java
@@ -0,0 +1,71 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.valuation.Valuation;
+
+import java.util.Objects;
+import java.util.Set;
+
+public final class ConstantTerm<T> extends AbstractTerm<T> {
+        private final T value;
+
+        public ConstantTerm(Class<T> type, T value) {
+                super(type);
+                if (value != null && !type.isInstance(value)) {
+                        throw new IllegalArgumentException("Value %s is not an instance of %s".formatted(value, type.getName()));
+                }
+                this.value = value;
+        }
+
+        public T getValue() {
+                return value;
+        }
+
+        @Override
+        public T evaluate(Valuation valuation) {
+                return getValue();
+        }
+
+        @Override
+        public Term<T> substitute(Substitution substitution) {
+                return this;
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherConstantTerm = (ConstantTerm<?>) other;
+                return Objects.equals(value, otherConstantTerm.value);
+        }
+
+        @Override
+        public Set<AnyDataVariable> getInputVariables() {
+                return Set.of();
+        }
+
+        @Override
+        public String toString() {
+                return value.toString();
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                ConstantTerm<?> that = (ConstantTerm<?>) o;
+                return Objects.equals(value, that.value);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(value);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java
new file mode 100644
index 00000000..00950360
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java
@@ -0,0 +1,82 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.valuation.Valuation;
+
+import java.util.Objects;
+
+public final class DataVariable<T> extends AnyDataVariable implements Term<T> {
+        private final Class<T> type;
+
+        DataVariable(String name, Class<T> type) {
+                super(name);
+                this.type = type;
+        }
+
+        @Override
+        public Class<T> getType() {
+                return type;
+        }
+
+        @Override
+        public DataVariable<T> renew(@Nullable String name) {
+                return new DataVariable<>(name, type);
+        }
+
+        @Override
+        public DataVariable<T> renew() {
+                return renew(getExplicitName());
+        }
+
+        @Override
+        public <U> DataVariable<U> asDataVariable(Class<U> newType) {
+                if (!getType().equals(newType)) {
+                        throw new IllegalStateException("%s is not of type %s but of type %s".formatted(this, newType.getName(),
+                                        getType().getName()));
+                }
+                @SuppressWarnings("unchecked")
+                var result = (DataVariable<U>) this;
+                return result;
+        }
+
+        @Override
+        public T evaluate(Valuation valuation) {
+                return valuation.getValue(this);
+        }
+
+        @Override
+        public Term<T> substitute(Substitution substitution) {
+                return substitution.getTypeSafeSubstitute(this);
+        }
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                return other instanceof DataVariable<?> dataVariable && helper.variableEqual(this, dataVariable);
+        }
+
+        public Literal assign(AssignedValue<T> value) {
+                return value.toLiteral(this);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                DataVariable<?> that = (DataVariable<?>) o;
+                return type.equals(that.type);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), type);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java
new file mode 100644
index 00000000..657cb631
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java
@@ -0,0 +1,108 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import java.util.Comparator;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+public class ExtremeValueAggregator<T> implements StatefulAggregator<T, T> {
+        private final Class<T> type;
+        private final T emptyResult;
+        private final Comparator<T> comparator;
+
+        public ExtremeValueAggregator(Class<T> type, T emptyResult) {
+                this(type, emptyResult, null);
+        }
+
+        public ExtremeValueAggregator(Class<T> type, T emptyResult, Comparator<T> comparator) {
+                this.type = type;
+                this.emptyResult = emptyResult;
+                this.comparator = comparator;
+        }
+
+        @Override
+        public Class<T> getResultType() {
+                return getInputType();
+        }
+
+        @Override
+        public Class<T> getInputType() {
+                return type;
+        }
+
+        @Override
+        public StatefulAggregate<T, T> createEmptyAggregate() {
+                return new Aggregate();
+        }
+
+        @Override
+        public T getEmptyResult() {
+                return emptyResult;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                ExtremeValueAggregator<?> that = (ExtremeValueAggregator<?>) o;
+                return type.equals(that.type) && Objects.equals(emptyResult, that.emptyResult) && Objects.equals(comparator,
+                                that.comparator);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(type, emptyResult, comparator);
+        }
+
+        private class Aggregate implements StatefulAggregate<T, T> {
+                private final SortedMap<T, Integer> values;
+
+                private Aggregate() {
+                        values = new TreeMap<>(comparator);
+                }
+
+                private Aggregate(Aggregate other) {
+                        values = new TreeMap<>(other.values);
+                }
+
+                @Override
+                public void add(T value) {
+                        values.compute(value, (ignoredValue, currentCount) -> currentCount == null ? 1 : currentCount + 1);
+                }
+
+                @Override
+                public void remove(T value) {
+                        values.compute(value, (theValue, currentCount) -> {
+                                if (currentCount == null || currentCount <= 0) {
+                                        throw new IllegalStateException("Invalid count %d for value %s".formatted(currentCount, theValue));
+                                }
+                                return currentCount.equals(1) ? null : currentCount - 1;
+                        });
+                }
+
+                @Override
+                public T getResult() {
+                        return isEmpty() ? emptyResult : values.firstKey();
+                }
+
+                @Override
+                public boolean isEmpty() {
+                        return values.isEmpty();
+                }
+
+                @Override
+                public StatefulAggregate<T, T> deepCopy() {
+                        return new Aggregate(this);
+                }
+
+                @Override
+                public boolean contains(T value) {
+                        return StatefulAggregate.super.contains(value);
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java
new file mode 100644
index 00000000..a2f3261f
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java
@@ -0,0 +1,60 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.literal.ConstantLiteral;
+import tools.refinery.store.query.literal.EquivalenceLiteral;
+
+import java.util.Optional;
+
+public final class NodeVariable extends Variable {
+        NodeVariable(@Nullable String name) {
+                super(name);
+        }
+
+        @Override
+        public Optional<Class<?>> tryGetType() {
+                return Optional.empty();
+        }
+
+        @Override
+        public boolean isUnifiable() {
+                return true;
+        }
+
+        @Override
+        public NodeVariable renew(@Nullable String name) {
+                return Variable.of(name);
+        }
+
+        @Override
+        public NodeVariable renew() {
+                return renew(getExplicitName());
+        }
+
+        @Override
+        public NodeVariable asNodeVariable() {
+                return this;
+        }
+
+        @Override
+        public <T> DataVariable<T> asDataVariable(Class<T> type) {
+                throw new IllegalStateException("%s is a node variable".formatted(this));
+        }
+
+        public ConstantLiteral isConstant(int value) {
+                return new ConstantLiteral(this, value);
+        }
+
+        public EquivalenceLiteral isEquivalent(NodeVariable other) {
+                return new EquivalenceLiteral(true, this, other);
+        }
+
+        public EquivalenceLiteral notEquivalent(NodeVariable other) {
+                return new EquivalenceLiteral(false, this, other);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
new file mode 100644
index 00000000..e5a0cdf1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
@@ -0,0 +1,60 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import java.util.Objects;
+import java.util.Optional;
+
+public class Parameter {
+        public static final Parameter NODE_OUT = new Parameter(null, ParameterDirection.OUT);
+
+        private final Class<?> dataType;
+        private final ParameterDirection direction;
+
+        public Parameter(Class<?> dataType, ParameterDirection direction) {
+                this.dataType = dataType;
+                this.direction = direction;
+        }
+
+        public boolean isNodeVariable() {
+                return dataType == null;
+        }
+
+        public boolean isDataVariable() {
+                return !isNodeVariable();
+        }
+
+        public Optional<Class<?>> tryGetType() {
+                return Optional.ofNullable(dataType);
+        }
+
+        public ParameterDirection getDirection() {
+                return direction;
+        }
+
+        public boolean isAssignable(Variable variable) {
+                if (variable instanceof AnyDataVariable dataVariable) {
+                        return dataVariable.getType().equals(dataType);
+                } else if (variable instanceof NodeVariable) {
+                        return !isDataVariable();
+                } else {
+                        throw new IllegalArgumentException("Unknown variable " + variable);
+                }
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Parameter parameter = (Parameter) o;
+                return Objects.equals(dataType, parameter.dataType) && direction == parameter.direction;
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(dataType, direction);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java
new file mode 100644
index 00000000..cd0739be
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+public enum ParameterDirection {
+        OUT("@Out"),
+        IN("@In");
+
+        private final String name;
+
+        ParameterDirection(String name) {
+                this.name = name;
+        }
+
+        @Override
+        public String toString() {
+                return name;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java
new file mode 100644
index 00000000..ab310556
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+public interface StatefulAggregate<R, T> {
+        void add(T value);
+
+        void remove(T value);
+
+        R getResult();
+
+        boolean isEmpty();
+
+        StatefulAggregate<R, T> deepCopy();
+
+        default boolean contains(T value) {
+                throw new UnsupportedOperationException();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java
new file mode 100644
index 00000000..df746a90
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java
@@ -0,0 +1,28 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import java.util.stream.Stream;
+
+public interface StatefulAggregator<R, T> extends Aggregator<R, T> {
+        StatefulAggregate<R, T> createEmptyAggregate();
+
+        @Override
+        default R aggregateStream(Stream<T> stream) {
+                var accumulator = createEmptyAggregate();
+                var iterator = stream.iterator();
+                while (iterator.hasNext()) {
+                        var value = iterator.next();
+                        accumulator.add(value);
+                }
+                return accumulator.getResult();
+        }
+
+        @Override
+        default R getEmptyResult() {
+                return createEmptyAggregate().getResult();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java
new file mode 100644
index 00000000..a094919e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java
@@ -0,0 +1,25 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import java.util.stream.Stream;
+
+public interface StatelessAggregator<R, T> extends Aggregator<R, T> {
+        R add(R current, T value);
+
+        R remove(R current, T value);
+
+        @Override
+        default R aggregateStream(Stream<T> stream) {
+                var accumulator = getEmptyResult();
+                var iterator = stream.iterator();
+                while (iterator.hasNext()) {
+                        var value = iterator.next();
+                        accumulator = add(accumulator, value);
+                }
+                return accumulator;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java
new file mode 100644
index 00000000..e6818b88
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java
@@ -0,0 +1,26 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.literal.AssignLiteral;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.valuation.Valuation;
+
+public non-sealed interface Term<T> extends AnyTerm, AssignedValue<T> {
+        @Override
+        Class<T> getType();
+
+        T evaluate(Valuation valuation);
+
+        @Override
+        Term<T> substitute(Substitution substitution);
+
+        @Override
+        default Literal toLiteral(DataVariable<T> targetVariable) {
+                return new AssignLiteral<>(targetVariable, this);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java
new file mode 100644
index 00000000..a46ebe31
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java
@@ -0,0 +1,79 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.valuation.Valuation;
+
+import java.util.Objects;
+import java.util.Set;
+
+public abstract class UnaryTerm<R, T> extends AbstractTerm<R> {
+        private final Class<T> bodyType;
+        private final Term<T> body;
+
+        protected UnaryTerm(Class<R> type, Class<T> bodyType, Term<T> body) {
+                super(type);
+                if (!body.getType().equals(bodyType)) {
+                        throw new IllegalArgumentException("Expected body %s to be of type %s, got %s instead".formatted(body,
+                                        bodyType.getName(), body.getType().getName()));
+                }
+                this.bodyType = bodyType;
+                this.body = body;
+        }
+
+        public Class<T> getBodyType() {
+                return bodyType;
+        }
+
+        public Term<T> getBody() {
+                return body;
+        }
+
+        @Override
+        public R evaluate(Valuation valuation) {
+                var bodyValue = body.evaluate(valuation);
+                return bodyValue == null ? null : doEvaluate(bodyValue);
+        }
+
+        protected abstract R doEvaluate(T bodyValue);
+
+        @Override
+        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
+                if (!super.equalsWithSubstitution(helper, other)) {
+                        return false;
+                }
+                var otherUnaryTerm = (UnaryTerm<?, ?>) other;
+                return bodyType.equals(otherUnaryTerm.bodyType) && body.equalsWithSubstitution(helper, otherUnaryTerm.body);
+        }
+
+        @Override
+        public Term<R> substitute(Substitution substitution) {
+                return doSubstitute(substitution, body.substitute(substitution));
+        }
+
+        protected abstract Term<R> doSubstitute(Substitution substitution, Term<T> substitutedBody);
+
+        @Override
+        public Set<AnyDataVariable> getInputVariables() {
+                return body.getInputVariables();
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                UnaryTerm<?, ?> unaryTerm = (UnaryTerm<?, ?>) o;
+                return Objects.equals(bodyType, unaryTerm.bodyType) && Objects.equals(body, unaryTerm.body);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), bodyType, body);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java
new file mode 100644
index 00000000..a0268c8e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java
@@ -0,0 +1,84 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.dnf.DnfUtils;
+
+import java.util.Objects;
+import java.util.Optional;
+
+public abstract sealed class Variable permits AnyDataVariable, NodeVariable {
+        private final String explicitName;
+        private final String uniqueName;
+
+        protected Variable(String name) {
+                this.explicitName = name;
+                uniqueName = DnfUtils.generateUniqueName(name);
+        }
+
+        public abstract Optional<Class<?>> tryGetType();
+
+        public String getName() {
+                return explicitName == null ? uniqueName : explicitName;
+        }
+
+        protected String getExplicitName() {
+                return explicitName;
+        }
+
+        public boolean isExplicitlyNamed() {
+                return explicitName != null;
+        }
+
+        public String getUniqueName() {
+                return uniqueName;
+        }
+
+        public abstract boolean isUnifiable();
+
+        public abstract Variable renew(@Nullable String name);
+
+        public abstract Variable renew();
+
+        public abstract NodeVariable asNodeVariable();
+
+        public abstract <T> DataVariable<T> asDataVariable(Class<T> type);
+
+        @Override
+        public String toString() {
+                return getName();
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Variable variable = (Variable) o;
+                return Objects.equals(uniqueName, variable.uniqueName);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(uniqueName);
+        }
+
+        public static NodeVariable of(@Nullable String name) {
+                return new NodeVariable(name);
+        }
+
+        public static NodeVariable of() {
+                return of((String) null);
+        }
+
+        public static <T> DataVariable<T> of(@Nullable String name, Class<T> type) {
+                return new DataVariable<>(name, type);
+        }
+
+        public static <T> DataVariable<T> of(Class<T> type) {
+                return of(null, type);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java
new file mode 100644
index 00000000..f9e1c06f
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class BoolAndTerm extends BoolBinaryTerm {
+        public BoolAndTerm(Term<Boolean> left, Term<Boolean> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
+                                                                          Term<Boolean> substitutedRight) {
+                return new BoolAndTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
+                return leftValue && rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s && %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java
new file mode 100644
index 00000000..a85aa63a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.term.BinaryTerm;
+import tools.refinery.store.query.term.Term;
+
+public abstract class BoolBinaryTerm extends BinaryTerm<Boolean, Boolean, Boolean> {
+        protected BoolBinaryTerm(Term<Boolean> left, Term<Boolean> right) {
+                super(Boolean.class, Boolean.class, Boolean.class, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java
new file mode 100644
index 00000000..8d3382b3
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.UnaryTerm;
+
+public class BoolNotTerm extends UnaryTerm<Boolean, Boolean> {
+        protected BoolNotTerm(Term<Boolean> body) {
+                super(Boolean.class, Boolean.class, body);
+        }
+
+        @Override
+        protected Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedBody) {
+                return new BoolNotTerm(substitutedBody);
+        }
+
+        @Override
+        protected Boolean doEvaluate(Boolean bodyValue) {
+                return !bodyValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(!%s)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java
new file mode 100644
index 00000000..b5195d52
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class BoolOrTerm extends BoolBinaryTerm {
+        public BoolOrTerm(Term<Boolean> left, Term<Boolean> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
+                                                                          Term<Boolean> substitutedRight) {
+                return new BoolOrTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
+                return leftValue || rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s || %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java
new file mode 100644
index 00000000..fa54f686
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java
@@ -0,0 +1,35 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.Term;
+
+public final class BoolTerms {
+        private BoolTerms() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static Term<Boolean> constant(Boolean value) {
+                return new ConstantTerm<>(Boolean.class, value);
+        }
+
+        public static Term<Boolean> not(Term<Boolean> body) {
+                return new BoolNotTerm(body);
+        }
+
+        public static Term<Boolean> and(Term<Boolean> left, Term<Boolean> right) {
+                return new BoolAndTerm(left, right);
+        }
+
+        public static Term<Boolean> or(Term<Boolean> left, Term<Boolean> right) {
+                return new BoolOrTerm(left, right);
+        }
+
+        public static Term<Boolean> xor(Term<Boolean> left, Term<Boolean> right) {
+                return new BoolXorTerm(left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java
new file mode 100644
index 00000000..7478b8a5
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class BoolXorTerm extends BoolBinaryTerm {
+        public BoolXorTerm(Term<Boolean> left, Term<Boolean> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
+                                                                          Term<Boolean> substitutedRight) {
+                return new BoolXorTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
+                return leftValue ^ rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s ^^ %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java
new file mode 100644
index 00000000..5ca5a0a1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java
@@ -0,0 +1,19 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.term.BinaryTerm;
+import tools.refinery.store.query.term.Term;
+
+public abstract class ComparisonTerm<T> extends BinaryTerm<Boolean, T, T> {
+        protected ComparisonTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(Boolean.class, argumentType, argumentType, left, right);
+        }
+
+        public Class<T> getArgumentType() {
+                return getLeftType();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java
new file mode 100644
index 00000000..b8cf36f8
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class EqTerm<T> extends ComparisonTerm<T> {
+        public EqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return leftValue.equals(rightValue);
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new EqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s == %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java
new file mode 100644
index 00000000..b109eb1a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class GreaterEqTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
+        public GreaterEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return leftValue.compareTo(rightValue) >= 0;
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new GreaterEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s >= %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java
new file mode 100644
index 00000000..1b67f8b5
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class GreaterTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
+        public GreaterTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return leftValue.compareTo(rightValue) > 0;
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new GreaterTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s > %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java
new file mode 100644
index 00000000..1b34535f
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class LessEqTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
+        public LessEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return leftValue.compareTo(rightValue) <= 0;
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new LessEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s <= %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java
new file mode 100644
index 00000000..44e70902
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class LessTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
+        public LessTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return leftValue.compareTo(rightValue) < 0;
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new LessTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s < %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java
new file mode 100644
index 00000000..1f9734c4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.comparable;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class NotEqTerm<T> extends ComparisonTerm<T> {
+        public NotEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
+                super(argumentType, left, right);
+        }
+
+        @Override
+        protected Boolean doEvaluate(T leftValue, T rightValue) {
+                return !leftValue.equals(rightValue);
+        }
+
+        @Override
+        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
+                return new NotEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s != %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java
new file mode 100644
index 00000000..dbea3efc
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntAddTerm extends IntBinaryTerm {
+        public IntAddTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntAddTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return leftValue + rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s + %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java
new file mode 100644
index 00000000..27ced4e4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.term.BinaryTerm;
+import tools.refinery.store.query.term.Term;
+
+public abstract class IntBinaryTerm extends BinaryTerm<Integer, Integer, Integer> {
+        protected IntBinaryTerm(Term<Integer> left, Term<Integer> right) {
+                super(Integer.class, Integer.class, Integer.class, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java
new file mode 100644
index 00000000..2a35058c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntDivTerm extends IntBinaryTerm {
+        public IntDivTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntDivTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return rightValue == 0 ? null : leftValue / rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s / %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java
new file mode 100644
index 00000000..f81fc509
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntMaxTerm extends IntBinaryTerm {
+        public IntMaxTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntMaxTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return Math.max(rightValue, leftValue);
+        }
+
+        @Override
+        public String toString() {
+                return "max(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java
new file mode 100644
index 00000000..89182e26
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntMinTerm extends IntBinaryTerm {
+        public IntMinTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntMinTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return Math.min(rightValue, leftValue);
+        }
+
+        @Override
+        public String toString() {
+                return "min(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java
new file mode 100644
index 00000000..709aa5ba
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntMinusTerm extends IntUnaryTerm {
+        public IntMinusTerm(Term<Integer> body) {
+                super(body);
+        }
+
+        @Override
+        protected Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
+                return new IntMinusTerm(substitutedBody);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer bodyValue) {
+                return -bodyValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(-%s)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java
new file mode 100644
index 00000000..89d4c5f4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntMulTerm extends IntBinaryTerm {
+        public IntMulTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntMulTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return leftValue * rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s * %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java
new file mode 100644
index 00000000..aef83bb4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntPlusTerm extends IntUnaryTerm {
+        public IntPlusTerm(Term<Integer> body) {
+                super(body);
+        }
+
+        @Override
+        protected Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
+                return new IntPlusTerm(substitutedBody);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer bodyValue) {
+                return bodyValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(+%s)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java
new file mode 100644
index 00000000..d5af97a1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntPowTerm extends IntBinaryTerm {
+        public IntPowTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntPowTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return rightValue < 0 ? null : power(leftValue, rightValue);
+        }
+
+        private static int power(int base, int exponent) {
+                int accum = 1;
+                while (exponent > 0) {
+                        if (exponent % 2 == 1) {
+                                accum = accum * base;
+                        }
+                        base = base * base;
+                        exponent = exponent / 2;
+                }
+                return accum;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s ** %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java
new file mode 100644
index 00000000..2c27afb1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class IntSubTerm extends IntBinaryTerm {
+        public IntSubTerm(Term<Integer> left, Term<Integer> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
+                                                                          Term<Integer> substitutedRight) {
+                return new IntSubTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
+                return leftValue - rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s - %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java
new file mode 100644
index 00000000..cd718c53
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java
@@ -0,0 +1,40 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.term.StatelessAggregator;
+
+public final class IntSumAggregator implements StatelessAggregator<Integer, Integer> {
+        public static final IntSumAggregator INSTANCE = new IntSumAggregator();
+
+        private IntSumAggregator() {
+        }
+
+        @Override
+        public Class<Integer> getResultType() {
+                return Integer.class;
+        }
+
+        @Override
+        public Class<Integer> getInputType() {
+                return Integer.class;
+        }
+
+        @Override
+        public Integer getEmptyResult() {
+                return 0;
+        }
+
+        @Override
+        public Integer add(Integer current, Integer value) {
+                return current + value;
+        }
+
+        @Override
+        public Integer remove(Integer current, Integer value) {
+                return current - value;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java
new file mode 100644
index 00000000..acb98b94
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java
@@ -0,0 +1,94 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.term.Aggregator;
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.ExtremeValueAggregator;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.comparable.*;
+
+import java.util.Comparator;
+
+public final class IntTerms {
+        public static final Aggregator<Integer, Integer> INT_SUM = IntSumAggregator.INSTANCE;
+        public static final Aggregator<Integer, Integer> INT_MIN = new ExtremeValueAggregator<>(Integer.class,
+                        Integer.MAX_VALUE);
+        public static final Aggregator<Integer, Integer> INT_MAX = new ExtremeValueAggregator<>(Integer.class,
+                        Integer.MIN_VALUE, Comparator.reverseOrder());
+
+        private IntTerms() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static Term<Integer> constant(Integer value) {
+                return new ConstantTerm<>(Integer.class, value);
+        }
+
+        public static Term<Integer> plus(Term<Integer> body) {
+                return new IntPlusTerm(body);
+        }
+
+        public static Term<Integer> minus(Term<Integer> body) {
+                return new IntMinusTerm(body);
+        }
+
+        public static Term<Integer> add(Term<Integer> left, Term<Integer> right) {
+                return new IntAddTerm(left, right);
+        }
+
+        public static Term<Integer> sub(Term<Integer> left, Term<Integer> right) {
+                return new IntSubTerm(left, right);
+        }
+
+        public static Term<Integer> mul(Term<Integer> left, Term<Integer> right) {
+                return new IntMulTerm(left, right);
+        }
+
+        public static Term<Integer> div(Term<Integer> left, Term<Integer> right) {
+                return new IntDivTerm(left, right);
+        }
+
+        public static Term<Integer> pow(Term<Integer> left, Term<Integer> right) {
+                return new IntPowTerm(left, right);
+        }
+
+        public static Term<Integer> min(Term<Integer> left, Term<Integer> right) {
+                return new IntMinTerm(left, right);
+        }
+
+        public static Term<Integer> max(Term<Integer> left, Term<Integer> right) {
+                return new IntMaxTerm(left, right);
+        }
+
+        public static Term<Boolean> eq(Term<Integer> left, Term<Integer> right) {
+                return new EqTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Boolean> notEq(Term<Integer> left, Term<Integer> right) {
+                return new NotEqTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Boolean> less(Term<Integer> left, Term<Integer> right) {
+                return new LessTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Boolean> lessEq(Term<Integer> left, Term<Integer> right) {
+                return new LessEqTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Boolean> greater(Term<Integer> left, Term<Integer> right) {
+                return new GreaterTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Boolean> greaterEq(Term<Integer> left, Term<Integer> right) {
+                return new GreaterEqTerm<>(Integer.class, left, right);
+        }
+
+        public static Term<Integer> asInt(Term<Double> body) {
+                return new RealToIntTerm(body);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java
new file mode 100644
index 00000000..49b4c647
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.UnaryTerm;
+
+public abstract class IntUnaryTerm extends UnaryTerm<Integer, Integer> {
+        protected IntUnaryTerm(Term<Integer> body) {
+                super(Integer.class, Integer.class, body);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java
new file mode 100644
index 00000000..7d383562
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.UnaryTerm;
+
+public class RealToIntTerm extends UnaryTerm<Integer, Double> {
+        protected RealToIntTerm(Term<Double> body) {
+                super(Integer.class, Double.class, body);
+        }
+
+        @Override
+        protected Integer doEvaluate(Double bodyValue) {
+                return bodyValue.isNaN() ? null : bodyValue.intValue();
+        }
+
+        @Override
+        protected Term<Integer> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
+                return new RealToIntTerm(substitutedBody);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s as int)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java
new file mode 100644
index 00000000..2f53117a
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.UnaryTerm;
+
+public class IntToRealTerm extends UnaryTerm<Double, Integer> {
+        protected IntToRealTerm(Term<Integer> body) {
+                super(Double.class, Integer.class, body);
+        }
+
+        @Override
+        protected Term<Double> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
+                return new IntToRealTerm(substitutedBody);
+        }
+
+        @Override
+        protected Double doEvaluate(Integer bodyValue) {
+                return bodyValue.doubleValue();
+        }
+
+        @Override
+        public String toString() {
+                return "(%s as real)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java
new file mode 100644
index 00000000..33fc9e41
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealAddTerm extends RealBinaryTerm {
+        public RealAddTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealAddTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return leftValue + rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s + %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java
new file mode 100644
index 00000000..000f3623
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.term.BinaryTerm;
+import tools.refinery.store.query.term.Term;
+
+public abstract class RealBinaryTerm extends BinaryTerm<Double, Double, Double> {
+        protected RealBinaryTerm(Term<Double> left, Term<Double> right) {
+                super(Double.class, Double.class, Double.class, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java
new file mode 100644
index 00000000..1e55bf42
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealDivTerm extends RealBinaryTerm {
+        public RealDivTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealDivTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return leftValue / rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s / %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java
new file mode 100644
index 00000000..2a249496
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealMaxTerm extends RealBinaryTerm {
+        public RealMaxTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealMaxTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return Math.max(leftValue, rightValue);
+        }
+
+        @Override
+        public String toString() {
+                return "max(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java
new file mode 100644
index 00000000..2eb4cc1e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealMinTerm extends RealBinaryTerm {
+        public RealMinTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealMinTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return Math.min(leftValue, rightValue);
+        }
+
+        @Override
+        public String toString() {
+                return "min(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java
new file mode 100644
index 00000000..4afec7a1
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealMinusTerm extends RealUnaryTerm {
+        public RealMinusTerm(Term<Double> body) {
+                super(body);
+        }
+
+        @Override
+        protected Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
+                return new RealMinusTerm(substitutedBody);
+        }
+
+        @Override
+        protected Double doEvaluate(Double bodyValue) {
+                return -bodyValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(-%s)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java
new file mode 100644
index 00000000..ec95ac6f
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealMulTerm extends RealBinaryTerm {
+        public RealMulTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealMulTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return leftValue * rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s * %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java
new file mode 100644
index 00000000..64dd2e70
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealPlusTerm extends RealUnaryTerm {
+        public RealPlusTerm(Term<Double> body) {
+                super(body);
+        }
+
+        @Override
+        protected Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
+                return new RealPlusTerm(substitutedBody);
+        }
+
+        @Override
+        protected Double doEvaluate(Double bodyValue) {
+                return bodyValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(+%s)".formatted(getBody());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java
new file mode 100644
index 00000000..11c952ea
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealPowTerm extends RealBinaryTerm {
+        public RealPowTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealPowTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return Math.pow(leftValue, rightValue);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s ** %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java
new file mode 100644
index 00000000..8cc701ed
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+
+public class RealSubTerm extends RealBinaryTerm {
+        public RealSubTerm(Term<Double> left, Term<Double> right) {
+                super(left, right);
+        }
+
+        @Override
+        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
+                                                                         Term<Double> substitutedRight) {
+                return new RealSubTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        protected Double doEvaluate(Double leftValue, Double rightValue) {
+                return leftValue - rightValue;
+        }
+
+        @Override
+        public String toString() {
+                return "(%s - %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java
new file mode 100644
index 00000000..d21048e9
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java
@@ -0,0 +1,90 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.term.StatefulAggregate;
+import tools.refinery.store.query.term.StatefulAggregator;
+
+import java.util.Map;
+import java.util.TreeMap;
+
+public final class RealSumAggregator implements StatefulAggregator<Double, Double> {
+        public static final RealSumAggregator INSTANCE = new RealSumAggregator();
+
+        private RealSumAggregator() {
+        }
+
+        @Override
+        public Class<Double> getResultType() {
+                return Double.class;
+        }
+
+        @Override
+        public Class<Double> getInputType() {
+                return Double.class;
+        }
+
+        @Override
+        public StatefulAggregate<Double, Double> createEmptyAggregate() {
+                return new Aggregate();
+        }
+
+        @Override
+        public Double getEmptyResult() {
+                return 0d;
+        }
+
+        private static class Aggregate implements StatefulAggregate<Double, Double> {
+                private final Map<Double, Integer> values;
+
+                public Aggregate() {
+                        values = new TreeMap<>();
+                }
+
+                private Aggregate(Aggregate other) {
+                        values = new TreeMap<>(other.values);
+                }
+
+                @Override
+                public void add(Double value) {
+                        values.compute(value, (ignoredValue, currentCount) -> currentCount == null ? 1 : currentCount + 1);
+                }
+
+                @Override
+                public void remove(Double value) {
+                        values.compute(value, (theValue, currentCount) -> {
+                                if (currentCount == null || currentCount <= 0) {
+                                        throw new IllegalStateException("Invalid count %d for value %f".formatted(currentCount, theValue));
+                                }
+                                return currentCount.equals(1) ? null : currentCount - 1;
+                        });
+                }
+
+                @Override
+                public Double getResult() {
+                        return values.entrySet()
+                                        .stream()
+                                        .mapToDouble(entry -> entry.getKey() * entry.getValue())
+                                        .reduce(Double::sum)
+                                        .orElse(0d);
+                }
+
+                @Override
+                public boolean isEmpty() {
+                        return values.isEmpty();
+                }
+
+                @Override
+                public StatefulAggregate<Double, Double> deepCopy() {
+                        return new Aggregate(this);
+                }
+
+                @Override
+                public boolean contains(Double value) {
+                        return values.containsKey(value);
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java
new file mode 100644
index 00000000..79220358
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java
@@ -0,0 +1,94 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.term.Aggregator;
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.ExtremeValueAggregator;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.comparable.*;
+
+import java.util.Comparator;
+
+public final class RealTerms {
+        public static final Aggregator<Double, Double> REAL_SUM = RealSumAggregator.INSTANCE;
+        public static final Aggregator<Double, Double> REAL_MIN = new ExtremeValueAggregator<>(Double.class,
+                        Double.POSITIVE_INFINITY);
+        public static final Aggregator<Double, Double> REAL_MAX = new ExtremeValueAggregator<>(Double.class,
+                        Double.NEGATIVE_INFINITY, Comparator.reverseOrder());
+
+        private RealTerms() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static Term<Double> constant(Double value) {
+                return new ConstantTerm<>(Double.class, value);
+        }
+
+        public static Term<Double> plus(Term<Double> body) {
+                return new RealPlusTerm(body);
+        }
+
+        public static Term<Double> minus(Term<Double> body) {
+                return new RealMinusTerm(body);
+        }
+
+        public static Term<Double> add(Term<Double> left, Term<Double> right) {
+                return new RealAddTerm(left, right);
+        }
+
+        public static Term<Double> sub(Term<Double> left, Term<Double> right) {
+                return new RealSubTerm(left, right);
+        }
+
+        public static Term<Double> mul(Term<Double> left, Term<Double> right) {
+                return new RealMulTerm(left, right);
+        }
+
+        public static Term<Double> div(Term<Double> left, Term<Double> right) {
+                return new RealDivTerm(left, right);
+        }
+
+        public static Term<Double> pow(Term<Double> left, Term<Double> right) {
+                return new RealPowTerm(left, right);
+        }
+
+        public static Term<Double> min(Term<Double> left, Term<Double> right) {
+                return new RealMinTerm(left, right);
+        }
+
+        public static Term<Double> max(Term<Double> left, Term<Double> right) {
+                return new RealMaxTerm(left, right);
+        }
+
+        public static Term<Boolean> eq(Term<Double> left, Term<Double> right) {
+                return new EqTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Boolean> notEq(Term<Double> left, Term<Double> right) {
+                return new NotEqTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Boolean> less(Term<Double> left, Term<Double> right) {
+                return new LessTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Boolean> lessEq(Term<Double> left, Term<Double> right) {
+                return new LessEqTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Boolean> greater(Term<Double> left, Term<Double> right) {
+                return new GreaterTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Boolean> greaterEq(Term<Double> left, Term<Double> right) {
+                return new GreaterEqTerm<>(Double.class, left, right);
+        }
+
+        public static Term<Double> asReal(Term<Integer> body) {
+                return new IntToRealTerm(body);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java
new file mode 100644
index 00000000..d41c4ed9
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.UnaryTerm;
+
+public abstract class RealUnaryTerm extends UnaryTerm<Double, Double> {
+        protected RealUnaryTerm(Term<Double> body) {
+                super(Double.class, Double.class, body);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java
new file mode 100644
index 00000000..68905f51
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public class UpperCardinalityAddTerm extends UpperCardinalityBinaryTerm {
+        protected UpperCardinalityAddTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                super(left, right);
+        }
+
+        @Override
+        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
+                return leftValue.add(rightValue);
+        }
+
+        @Override
+        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
+                return new UpperCardinalityAddTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s + %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java
new file mode 100644
index 00000000..0cf8fe44
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.term.BinaryTerm;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public abstract class UpperCardinalityBinaryTerm extends BinaryTerm<UpperCardinality, UpperCardinality,
+                UpperCardinality> {
+        protected UpperCardinalityBinaryTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                super(UpperCardinality.class, UpperCardinality.class, UpperCardinality.class, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java
new file mode 100644
index 00000000..ff75f64e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public class UpperCardinalityMaxTerm extends UpperCardinalityBinaryTerm {
+        protected UpperCardinalityMaxTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                super(left, right);
+        }
+
+        @Override
+        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
+                return leftValue.max(rightValue);
+        }
+
+        @Override
+        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
+                return new UpperCardinalityMaxTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "max(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java
new file mode 100644
index 00000000..1e89e9f4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public class UpperCardinalityMinTerm extends UpperCardinalityBinaryTerm {
+        protected UpperCardinalityMinTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                super(left, right);
+        }
+
+        @Override
+        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
+                return leftValue.min(rightValue);
+        }
+
+        @Override
+        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
+                return new UpperCardinalityMinTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "min(%s, %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java
new file mode 100644
index 00000000..3b4970f4
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public class UpperCardinalityMulTerm extends UpperCardinalityBinaryTerm {
+        protected UpperCardinalityMulTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                super(left, right);
+        }
+
+        @Override
+        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
+                return leftValue.multiply(rightValue);
+        }
+
+        @Override
+        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
+                return new UpperCardinalityMulTerm(substitutedLeft, substitutedRight);
+        }
+
+        @Override
+        public String toString() {
+                return "(%s * %s)".formatted(getLeft(), getRight());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java
new file mode 100644
index 00000000..5bbd3081
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java
@@ -0,0 +1,86 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.term.StatefulAggregate;
+import tools.refinery.store.query.term.StatefulAggregator;
+import tools.refinery.store.representation.cardinality.FiniteUpperCardinality;
+import tools.refinery.store.representation.cardinality.UnboundedUpperCardinality;
+import tools.refinery.store.representation.cardinality.UpperCardinalities;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+public class UpperCardinalitySumAggregator implements StatefulAggregator<UpperCardinality, UpperCardinality> {
+        public static final UpperCardinalitySumAggregator INSTANCE = new UpperCardinalitySumAggregator();
+
+        private UpperCardinalitySumAggregator() {
+        }
+
+        @Override
+        public Class<UpperCardinality> getResultType() {
+                return UpperCardinality.class;
+        }
+
+        @Override
+        public Class<UpperCardinality> getInputType() {
+                return UpperCardinality.class;
+        }
+
+        @Override
+        public StatefulAggregate<UpperCardinality, UpperCardinality> createEmptyAggregate() {
+                return new Aggregate();
+        }
+
+        private static class Aggregate implements StatefulAggregate<UpperCardinality, UpperCardinality> {
+                private int sumFiniteUpperBounds;
+                private int countUnbounded;
+
+                public Aggregate() {
+                        this(0, 0);
+                }
+
+                private Aggregate(int sumFiniteUpperBounds, int countUnbounded) {
+                        this.sumFiniteUpperBounds = sumFiniteUpperBounds;
+                        this.countUnbounded = countUnbounded;
+                }
+
+                @Override
+                public void add(UpperCardinality value) {
+                        if (value instanceof FiniteUpperCardinality finiteUpperCardinality) {
+                                sumFiniteUpperBounds += finiteUpperCardinality.finiteUpperBound();
+                        } else if (value instanceof UnboundedUpperCardinality) {
+                                countUnbounded += 1;
+                        } else {
+                                throw new IllegalArgumentException("Unknown UpperCardinality: " + value);
+                        }
+                }
+
+                @Override
+                public void remove(UpperCardinality value) {
+                        if (value instanceof FiniteUpperCardinality finiteUpperCardinality) {
+                                sumFiniteUpperBounds -= finiteUpperCardinality.finiteUpperBound();
+                        } else if (value instanceof UnboundedUpperCardinality) {
+                                countUnbounded -= 1;
+                        } else {
+                                throw new IllegalArgumentException("Unknown UpperCardinality: " + value);
+                        }
+                }
+
+                @Override
+                public UpperCardinality getResult() {
+                        return countUnbounded > 0 ? UpperCardinalities.UNBOUNDED : UpperCardinalities.valueOf(sumFiniteUpperBounds);
+                }
+
+                @Override
+                public boolean isEmpty() {
+                        return sumFiniteUpperBounds == 0 && countUnbounded == 0;
+                }
+
+                @Override
+                public StatefulAggregate<UpperCardinality, UpperCardinality> deepCopy() {
+                        return new Aggregate(sumFiniteUpperBounds, countUnbounded);
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java
new file mode 100644
index 00000000..13914f2d
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java
@@ -0,0 +1,73 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import tools.refinery.store.query.term.Aggregator;
+import tools.refinery.store.query.term.ConstantTerm;
+import tools.refinery.store.query.term.ExtremeValueAggregator;
+import tools.refinery.store.query.term.Term;
+import tools.refinery.store.query.term.comparable.*;
+import tools.refinery.store.representation.cardinality.UpperCardinalities;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+import java.util.Comparator;
+
+public final class UpperCardinalityTerms {
+        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_SUM =
+                        UpperCardinalitySumAggregator.INSTANCE;
+        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_MIN =
+                        new ExtremeValueAggregator<>(UpperCardinality.class, UpperCardinalities.UNBOUNDED);
+        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_MAX =
+                        new ExtremeValueAggregator<>(UpperCardinality.class, UpperCardinalities.ZERO, Comparator.reverseOrder());
+
+        private UpperCardinalityTerms() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static Term<UpperCardinality> constant(UpperCardinality value) {
+                return new ConstantTerm<>(UpperCardinality.class, value);
+        }
+
+        public static Term<UpperCardinality> add(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new UpperCardinalityAddTerm(left, right);
+        }
+
+        public static Term<UpperCardinality> mul(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new UpperCardinalityMulTerm(left, right);
+        }
+
+        public static Term<UpperCardinality> min(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new UpperCardinalityMinTerm(left, right);
+        }
+
+        public static Term<UpperCardinality> max(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new UpperCardinalityMaxTerm(left, right);
+        }
+
+        public static Term<Boolean> eq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new EqTerm<>(UpperCardinality.class, left, right);
+        }
+
+        public static Term<Boolean> notEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new NotEqTerm<>(UpperCardinality.class, left, right);
+        }
+
+        public static Term<Boolean> less(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new LessTerm<>(UpperCardinality.class, left, right);
+        }
+
+        public static Term<Boolean> lessEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new LessEqTerm<>(UpperCardinality.class, left, right);
+        }
+
+        public static Term<Boolean> greater(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new GreaterTerm<>(UpperCardinality.class, left, right);
+        }
+
+        public static Term<Boolean> greaterEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
+                return new GreaterEqTerm<>(UpperCardinality.class, left, right);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/utils/OrderStatisticTree.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/utils/OrderStatisticTree.java
new file mode 100644
index 00000000..b568b99d
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/utils/OrderStatisticTree.java
@@ -0,0 +1,754 @@
+/*
+ * Copyright (c) 2021 Rodion Efremov
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+package tools.refinery.store.query.utils;
+
+import java.util.*;
+
+/**
+ * This class implements an order statistic tree which is based on AVL-trees.
+ * <p>
+ * This class was copied into <i>Refinery</i> from
+ * <a href="https://github.com/coderodde/OrderStatisticTree/tree/546c343b9f5d868e394a079ff32691c9dbfd83e3">https://github.com/coderodde/OrderStatisticTree</a>
+ * and is available under the
+ * <a href="https://github.com/coderodde/OrderStatisticTree/blob/master/LICENSE">MIT License</a>.
+ * We also incorporated changes by <a href="https://github.com/coderodde/OrderStatisticTree/issues/3">Eugene Schava</a>
+ * and cleaned up some linter warnings.
+ *
+ * @param <T> the actual element type.
+ * @author Rodion "rodde" Efremov
+ * @version based on 1.6 (Feb 11, 2016)
+ */
+public class OrderStatisticTree<T extends Comparable<? super T>> implements Set<T> {
+
+        @Override
+        public Iterator<T> iterator() {
+                return new TreeIterator();
+        }
+
+        private final class TreeIterator implements Iterator<T> {
+
+                private Node<T> previousNode;
+                private Node<T> nextNode;
+                private int expectedModCount = modCount;
+
+                TreeIterator() {
+                        if (root == null) {
+                                nextNode = null;
+                        } else {
+                                nextNode = minimumNode(root);
+                        }
+                }
+
+                @Override
+                public boolean hasNext() {
+                        return nextNode != null;
+                }
+
+                @Override
+                public T next() {
+                        if (nextNode == null) {
+                                throw new NoSuchElementException("Iteration exceeded.");
+                        }
+
+                        checkConcurrentModification();
+                        T datum = nextNode.key;
+                        previousNode = nextNode;
+                        nextNode = successorOf(nextNode);
+                        return datum;
+                }
+
+                @Override
+                public void remove() {
+                        if (previousNode == null) {
+                                throw new IllegalStateException(
+                                                nextNode == null ?
+                                                                "Not a single call to next(); nothing to remove." :
+                                                                "Removing the same element twice."
+                                );
+                        }
+
+                        checkConcurrentModification();
+
+                        Node<T> x = deleteNode(previousNode);
+                        fixAfterModification(x, false);
+
+                        if (x == nextNode) {
+                                nextNode = previousNode;
+                        }
+
+                        expectedModCount = ++modCount;
+                        size--;
+                        previousNode = null;
+                }
+
+                private void checkConcurrentModification() {
+                        if (expectedModCount != modCount) {
+                                throw new ConcurrentModificationException(
+                                                "The set was modified while iterating.");
+                        }
+                }
+
+                private Node<T> successorOf(Node<T> node) {
+                        if (node.right != null) {
+                                node = node.right;
+
+                                while (node.left != null) {
+                                        node = node.left;
+                                }
+
+                                return node;
+                        }
+
+                        Node<T> parent = node.parent;
+
+                        while (parent != null && parent.right == node) {
+                                node = parent;
+                                parent = parent.parent;
+                        }
+
+                        return parent;
+                }
+        }
+
+        @Override
+        public Object[] toArray() {
+                Object[] array = new Object[size];
+                Iterator<T> iterator = iterator();
+                int index = 0;
+
+                while (iterator.hasNext()) {
+                        array[index++] = iterator.next();
+                }
+
+                return array;
+        }
+
+        @Override
+        public <U> U[] toArray(U[] a) {
+                Iterator<T> iterator = iterator();
+
+                if (size > a.length) {
+                        a = Arrays.copyOf(a, size);
+                }
+
+                int index = 0;
+
+                for (; index < size; ++index) {
+                        @SuppressWarnings("unchecked")
+                        var convertedValue = (U) iterator.next();
+                        a[index] = convertedValue;
+                }
+
+                if (index < a.length) {
+                        a[index] = null;
+                }
+
+                return a;
+        }
+
+        @Override
+        public boolean containsAll(Collection<?> c) {
+                for (Object element : c) {
+                        if (!contains(element)) {
+                                return false;
+                        }
+                }
+
+                return true;
+        }
+
+        @Override
+        public boolean addAll(Collection<? extends T> c) {
+                boolean modified = false;
+
+                for (T element : c) {
+                        if (add(element)) {
+                                modified = true;
+                        }
+                }
+
+                return modified;
+        }
+
+        @Override
+        public boolean retainAll(Collection<?> c) {
+                if (!c.getClass().equals(HashSet.class)) {
+                        c = new HashSet<>(c);
+                }
+
+                Iterator<T> iterator = iterator();
+                boolean modified = false;
+
+                while (iterator.hasNext()) {
+                        T element = iterator.next();
+
+                        if (!c.contains(element)) {
+                                iterator.remove();
+                                modified = true;
+                        }
+                }
+
+                return modified;
+        }
+
+        @Override
+        public boolean removeAll(Collection<?> c) {
+                boolean modified = false;
+
+                for (Object element : c) {
+                        if (remove(element)) {
+                                modified = true;
+                        }
+                }
+
+                return modified;
+        }
+
+        private static final class Node<T> {
+                T key;
+
+                Node<T> parent;
+                Node<T> left;
+                Node<T> right;
+
+                int height;
+                int count;
+
+                Node(T key) {
+                        this.key = key;
+                }
+        }
+
+        private Node<T> root;
+        private int size;
+        private int modCount;
+
+        @Override
+        public boolean add(T element) {
+                Objects.requireNonNull(element, "The input element is null.");
+
+                if (root == null) {
+                        root = new Node<>(element);
+                        size = 1;
+                        modCount++;
+                        return true;
+                }
+
+                Node<T> parent = null;
+                Node<T> node = root;
+                int cmp;
+
+                while (node != null) {
+                        cmp = element.compareTo(node.key);
+
+                        if (cmp == 0) {
+                                // The element is already in this tree.
+                                return false;
+                        }
+
+                        parent = node;
+
+                        if (cmp < 0) {
+                                node = node.left;
+                        } else {
+                                node = node.right;
+                        }
+                }
+
+                Node<T> newnode = new Node<>(element);
+
+                if (element.compareTo(parent.key) < 0) {
+                        parent.left = newnode;
+                } else {
+                        parent.right = newnode;
+                }
+
+                newnode.parent = parent;
+                size++;
+                modCount++;
+                Node<T> hi = parent;
+                Node<T> lo = newnode;
+
+                while (hi != null) {
+                        if (hi.left == lo) {
+                                hi.count++;
+                        }
+
+                        lo = hi;
+                        hi = hi.parent;
+                }
+
+                fixAfterModification(newnode, true);
+                return true;
+        }
+
+        @Override
+        public boolean contains(Object o) {
+                @SuppressWarnings("unchecked")
+                T element = (T) o;
+                Node<T> x = root;
+                int cmp;
+
+                while (x != null && (cmp = element.compareTo(x.key)) != 0) {
+                        if (cmp < 0) {
+                                x = x.left;
+                        } else {
+                                x = x.right;
+                        }
+                }
+
+                return x != null;
+        }
+
+        @Override
+        public boolean remove(Object o) {
+                @SuppressWarnings("unchecked")
+                T element = (T) o;
+                Node<T> x = root;
+                int cmp;
+
+                while (x != null && (cmp = element.compareTo(x.key)) != 0) {
+                        if (cmp < 0) {
+                                x = x.left;
+                        } else {
+                                x = x.right;
+                        }
+                }
+
+                if (x == null) {
+                        return false;
+                }
+
+                x = deleteNode(x);
+                fixAfterModification(x, false);
+                size--;
+                modCount++;
+                return true;
+        }
+
+        public T get(int index) {
+                checkIndex(index);
+                Node<T> node = root;
+
+                while (true) {
+                        if (index > node.count) {
+                                index -= node.count + 1;
+                                node = node.right;
+                        } else if (index < node.count) {
+                                node = node.left;
+                        } else {
+                                return node.key;
+                        }
+                }
+        }
+
+        public int indexOf(T element) {
+                Node<T> node = root;
+
+                if (root == null) {
+                        return -1;
+                }
+
+                int rank = root.count;
+                int cmp;
+
+                while (true) {
+                        if ((cmp = element.compareTo(node.key)) < 0) {
+                                if (node.left == null) {
+                                        return -1;
+                                }
+
+                                rank -= (node.count - node.left.count);
+                                node = node.left;
+                        } else if (cmp > 0) {
+                                if (node.right == null) {
+                                        return -1;
+                                }
+
+                                rank += 1 + node.right.count;
+                                node = node.right;
+                        } else {
+                                return rank;
+                        }
+                }
+        }
+
+        @Override
+        public int size() {
+                return size;
+        }
+
+        @Override
+        public boolean isEmpty() {
+                return size == 0;
+        }
+
+        @Override
+        public void clear() {
+                modCount += size;
+                root = null;
+                size = 0;
+        }
+
+
+        private void checkIndex(int index) {
+                if (index < 0) {
+                        throw new IndexOutOfBoundsException(
+                                        "The input index is negative: " + index);
+                }
+
+                if (index >= size) {
+                        throw new IndexOutOfBoundsException(
+                                        "The input index is too large: " + index +
+                                                        ", the size of this tree is " + size);
+                }
+        }
+
+        @SuppressWarnings("squid:S3776")
+        private Node<T> deleteNode(Node<T> node) {
+                if (node.left == null && node.right == null) {
+                        // 'node' has no children.
+                        Node<T> parent = node.parent;
+
+                        if (parent == null) {
+                                // 'node' is the root node of this tree.
+                                root = null;
+                                ++modCount;
+                                return node;
+                        }
+
+                        Node<T> lo = node;
+                        Node<T> hi = parent;
+
+                        while (hi != null) {
+                                if (hi.left == lo) {
+                                        hi.count--;
+                                }
+
+                                lo = hi;
+                                hi = hi.parent;
+                        }
+
+                        if (node == parent.left) {
+                                parent.left = null;
+                        } else {
+                                parent.right = null;
+                        }
+
+                        return node;
+                }
+
+                if (node.left != null && node.right != null) {
+                        // 'node' has both children.
+                        Node<T> successor = minimumNode(node.right);
+                        node.key = successor.key;
+                        Node<T> child = successor.right;
+                        Node<T> parent = successor.parent;
+
+                        if (parent.left == successor) {
+                                parent.left = child;
+                        } else {
+                                parent.right = child;
+                        }
+
+                        if (child != null) {
+                                child.parent = parent;
+                        }
+
+                        Node<T> lo = child;
+                        Node<T> hi = parent;
+
+                        while (hi != null) {
+                                if (hi.left == lo) {
+                                        hi.count--;
+                                }
+
+                                lo = hi;
+                                hi = hi.parent;
+                        }
+
+                        return successor;
+                }
+
+                Node<T> child;
+
+                // 'node' has only one child.
+                if (node.left != null) {
+                        child = node.left;
+                } else {
+                        child = node.right;
+                }
+
+                Node<T> parent = node.parent;
+                child.parent = parent;
+
+                if (parent == null) {
+                        root = child;
+                        return node;
+                }
+
+                if (node == parent.left) {
+                        parent.left = child;
+                } else {
+                        parent.right = child;
+                }
+
+                Node<T> hi = parent;
+                Node<T> lo = child;
+
+                while (hi != null) {
+                        if (hi.left == lo) {
+                                hi.count--;
+                        }
+
+                        lo = hi;
+                        hi = hi.parent;
+                }
+
+                return node;
+
+        }
+
+        private Node<T> minimumNode(Node<T> node) {
+                while (node.left != null) {
+                        node = node.left;
+                }
+
+                return node;
+        }
+
+        private int height(Node<T> node) {
+                return node == null ? -1 : node.height;
+        }
+
+        private Node<T> leftRotate(Node<T> node1) {
+                Node<T> node2 = node1.right;
+                node2.parent = node1.parent;
+                node1.parent = node2;
+                node1.right = node2.left;
+                node2.left = node1;
+
+                if (node1.right != null) {
+                        node1.right.parent = node1;
+                }
+
+                node1.height = Math.max(height(node1.left), height(node1.right)) + 1;
+                node2.height = Math.max(height(node2.left), height(node2.right)) + 1;
+                node2.count += node1.count + 1;
+                return node2;
+        }
+
+        private Node<T> rightRotate(Node<T> node1) {
+                Node<T> node2 = node1.left;
+                node2.parent = node1.parent;
+                node1.parent = node2;
+                node1.left = node2.right;
+                node2.right = node1;
+
+                if (node1.left != null) {
+                        node1.left.parent = node1;
+                }
+
+                node1.height = Math.max(height(node1.left), height(node1.right)) + 1;
+                node2.height = Math.max(height(node2.left), height(node2.right)) + 1;
+                node1.count -= node2.count + 1;
+                return node2;
+        }
+
+        private Node<T> rightLeftRotate(Node<T> node1) {
+                Node<T> node2 = node1.right;
+                node1.right = rightRotate(node2);
+                return leftRotate(node1);
+        }
+
+        private Node<T> leftRightRotate(Node<T> node1) {
+                Node<T> node2 = node1.left;
+                node1.left = leftRotate(node2);
+                return rightRotate(node1);
+        }
+
+        // Fixing an insertion: use insertionMode = true.
+        // Fixing a deletion: use insertionMode = false.
+        @SuppressWarnings("squid:S3776")
+        private void fixAfterModification(Node<T> node, boolean insertionMode) {
+                Node<T> parent = node.parent;
+                Node<T> grandParent;
+                Node<T> subTree;
+
+                while (parent != null) {
+                        if (height(parent.left) == height(parent.right) + 2) {
+                                grandParent = parent.parent;
+
+                                if (height(parent.left.left) >= height(parent.left.right)) {
+                                        subTree = rightRotate(parent);
+                                } else {
+                                        subTree = leftRightRotate(parent);
+                                }
+
+                                if (grandParent == null) {
+                                        root = subTree;
+                                } else if (grandParent.left == parent) {
+                                        grandParent.left = subTree;
+                                } else {
+                                        grandParent.right = subTree;
+                                }
+
+                                if (grandParent != null) {
+                                        grandParent.height = Math.max(
+                                                        height(grandParent.left),
+                                                        height(grandParent.right)) + 1;
+                                }
+
+                                if (insertionMode) {
+                                        // Whenever fixing after insertion, at most one rotation is
+                                        // required in order to maintain the balance.
+                                        return;
+                                }
+                        } else if (height(parent.right) == height(parent.left) + 2) {
+                                grandParent = parent.parent;
+
+                                if (height(parent.right.right) >= height(parent.right.left)) {
+                                        subTree = leftRotate(parent);
+                                } else {
+                                        subTree = rightLeftRotate(parent);
+                                }
+
+                                if (grandParent == null) {
+                                        root = subTree;
+                                } else if (grandParent.left == parent) {
+                                        grandParent.left = subTree;
+                                } else {
+                                        grandParent.right = subTree;
+                                }
+
+                                if (grandParent != null) {
+                                        grandParent.height =
+                                                        Math.max(height(grandParent.left),
+                                                                        height(grandParent.right)) + 1;
+                                }
+
+                                if (insertionMode) {
+                                        return;
+                                }
+                        }
+
+                        parent.height = Math.max(height(parent.left),
+                                        height(parent.right)) + 1;
+                        parent = parent.parent;
+                }
+        }
+
+        boolean isHealthy() {
+                if (root == null) {
+                        return true;
+                }
+
+                return !containsCycles()
+                                && heightsAreCorrect()
+                                && isBalanced()
+                                && isWellIndexed();
+        }
+
+        private boolean containsCycles() {
+                Set<Node<T>> visitedNodes = new HashSet<>();
+                return containsCycles(root, visitedNodes);
+        }
+
+        private boolean containsCycles(Node<T> current, Set<Node<T>> visitedNodes) {
+                if (current == null) {
+                        return false;
+                }
+
+                if (visitedNodes.contains(current)) {
+                        return true;
+                }
+
+                visitedNodes.add(current);
+
+                return containsCycles(current.left, visitedNodes)
+                                || containsCycles(current.right, visitedNodes);
+        }
+
+        private boolean heightsAreCorrect() {
+                return getHeight(root) == root.height;
+        }
+
+        private int getHeight(Node<T> node) {
+                if (node == null) {
+                        return -1;
+                }
+
+                int leftTreeHeight = getHeight(node.left);
+
+                if (leftTreeHeight == Integer.MIN_VALUE) {
+                        return Integer.MIN_VALUE;
+                }
+
+                int rightTreeHeight = getHeight(node.right);
+
+                if (rightTreeHeight == Integer.MIN_VALUE) {
+                        return Integer.MIN_VALUE;
+                }
+
+                if (node.height == Math.max(leftTreeHeight, rightTreeHeight) + 1) {
+                        return node.height;
+                }
+
+                return Integer.MIN_VALUE;
+        }
+
+        private boolean isBalanced() {
+                return isBalanced(root);
+        }
+
+        private boolean isBalanced(Node<T> node) {
+                if (node == null) {
+                        return true;
+                }
+
+                if (!isBalanced(node.left)) {
+                        return false;
+                }
+
+                if (!isBalanced(node.right)) {
+                        return false;
+                }
+
+                int leftHeight = height(node.left);
+                int rightHeight = height(node.right);
+
+                return Math.abs(leftHeight - rightHeight) < 2;
+        }
+
+        private boolean isWellIndexed() {
+                return size == count(root);
+        }
+
+        private int count(Node<T> node) {
+                if (node == null) {
+                        return 0;
+                }
+
+                int leftTreeSize = count(node.left);
+
+                if (leftTreeSize == Integer.MIN_VALUE) {
+                        return Integer.MIN_VALUE;
+                }
+
+                if (node.count != leftTreeSize) {
+                        return Integer.MIN_VALUE;
+                }
+
+                int rightTreeSize = count(node.right);
+
+                if (rightTreeSize == Integer.MIN_VALUE) {
+                        return Integer.MIN_VALUE;
+                }
+
+                return leftTreeSize + 1 + rightTreeSize;
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java
new file mode 100644
index 00000000..261ceaa5
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.valuation;
+
+import tools.refinery.store.query.term.AnyDataVariable;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Map;
+
+record MapBasedValuation(Map<AnyDataVariable, Object> values) implements Valuation {
+        @Override
+        public <T> T getValue(DataVariable<T> variable) {
+                if (!values.containsKey(variable)) {
+                        throw new IllegalArgumentException("No value for variable %s".formatted(variable));
+                }
+                var value = values.get(variable);
+                return variable.getType().cast(value);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java
new file mode 100644
index 00000000..fc8406aa
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.valuation;
+
+import tools.refinery.store.query.term.AnyDataVariable;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Set;
+
+public record RestrictedValuation(Valuation valuation, Set<AnyDataVariable> allowedVariables) implements Valuation {
+        @Override
+        public <T> T getValue(DataVariable<T> variable) {
+                if (!allowedVariables.contains(variable)) {
+                        throw new IllegalArgumentException("Variable %s is not in scope".formatted(variable));
+                }
+                return valuation.getValue(variable);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java
new file mode 100644
index 00000000..1c14112c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.valuation;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.DataVariable;
+
+public record SubstitutedValuation(Valuation originalValuation, Substitution substitution) implements Valuation {
+        @Override
+        public <T> T getValue(DataVariable<T> variable) {
+                return originalValuation.getValue(substitution.getTypeSafeSubstitute(variable));
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java
new file mode 100644
index 00000000..1588e957
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.valuation;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.AnyDataVariable;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Map;
+import java.util.Set;
+
+public interface Valuation {
+        <T> T getValue(DataVariable<T> variable);
+
+        default Valuation substitute(@Nullable Substitution substitution) {
+                if (substitution == null) {
+                        return this;
+                }
+                return new SubstitutedValuation(this, substitution);
+        }
+
+        default Valuation restrict(Set<? extends AnyDataVariable> allowedVariables) {
+                return new RestrictedValuation(this, Set.copyOf(allowedVariables));
+        }
+
+        static ValuationBuilder builder() {
+                return new ValuationBuilder();
+        }
+
+        static Valuation empty() {
+                return new MapBasedValuation(Map.of());
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java
new file mode 100644
index 00000000..7337dbc3
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java
@@ -0,0 +1,40 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.valuation;
+
+import tools.refinery.store.query.term.AnyDataVariable;
+import tools.refinery.store.query.term.DataVariable;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ValuationBuilder {
+        private final Map<AnyDataVariable, Object> values = new HashMap<>();
+
+        ValuationBuilder() {
+        }
+
+        public <T> ValuationBuilder put(DataVariable<T> variable, T value) {
+                return putChecked(variable, value);
+        }
+
+        public ValuationBuilder putChecked(AnyDataVariable variable, Object value) {
+                if (value != null && !variable.getType().isInstance(value)) {
+                        throw new IllegalArgumentException("Value %s is not an instance of %s"
+                                        .formatted(value, variable.getType().getName()));
+                }
+                if (values.containsKey(variable)) {
+                        throw new IllegalArgumentException("Already has value for variable %s".formatted(variable));
+                }
+                values.put(variable, value);
+                return this;
+        }
+
+        public Valuation build() {
+                return new MapBasedValuation(Collections.unmodifiableMap(values));
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
new file mode 100644
index 00000000..fd37604e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
@@ -0,0 +1,110 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.dnf.FunctionalDependency;
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+
+public abstract class AbstractFunctionView<T> extends SymbolView<T> {
+        private final List<Parameter> parameters;
+
+        protected AbstractFunctionView(Symbol<T> symbol, String name, Parameter outParameter) {
+                super(symbol, name);
+                parameters = createParameters(symbol.arity(), outParameter);
+        }
+
+        @Override
+        public Set<FunctionalDependency<Integer>> getFunctionalDependencies() {
+                var arity = getSymbol().arity();
+                var forEach = IntStream.range(0, arity).boxed().collect(Collectors.toUnmodifiableSet());
+                var unique = Set.of(arity);
+                return Set.of(new FunctionalDependency<>(forEach, unique));
+        }
+
+        @Override
+        public Set<ViewImplication> getImpliedRelationViews() {
+                var symbol = getSymbol();
+                var impliedIndices = IntStream.range(0, symbol.arity()).boxed().toList();
+                var keysView = new KeyOnlyView<>(symbol);
+                return Set.of(new ViewImplication(this, keysView, impliedIndices));
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, T value) {
+                return true;
+        }
+
+        protected Object forwardMapValue(T value) {
+                return value;
+        }
+
+        protected boolean valueEquals(T value, Object otherForwardMappedValue) {
+                return Objects.equals(otherForwardMappedValue, forwardMapValue(value));
+        }
+
+        @Override
+        public Object[] forwardMap(Tuple key, T value) {
+                int size = key.getSize();
+                Object[] result = new Object[size + 1];
+                for (int i = 0; i < size; i++) {
+                        result[i] = Tuple.of(key.get(i));
+                }
+                result[key.getSize()] = forwardMapValue(value);
+                return result;
+        }
+
+        @Override
+        public boolean get(Model model, Object[] tuple) {
+                int[] content = new int[tuple.length - 1];
+                for (int i = 0; i < tuple.length - 1; i++) {
+                        if (!(tuple[i] instanceof Tuple1 wrapper)) {
+                                return false;
+                        }
+                        content[i] = wrapper.value0();
+                }
+                Tuple key = Tuple.of(content);
+                var valueInTuple = tuple[tuple.length - 1];
+                T valueInMap = model.getInterpretation(getSymbol()).get(key);
+                return valueEquals(valueInMap, valueInTuple);
+        }
+
+        @Override
+        public List<Parameter> getParameters() {
+                return parameters;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                AbstractFunctionView<?> that = (AbstractFunctionView<?>) o;
+                return Objects.equals(parameters, that.parameters);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), parameters);
+        }
+
+        private static List<Parameter> createParameters(int symbolArity, Parameter outParameter) {
+                var parameters = new Parameter[symbolArity + 1];
+                Arrays.fill(parameters, Parameter.NODE_OUT);
+                parameters[symbolArity] = outParameter;
+                return List.of(parameters);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java
new file mode 100644
index 00000000..90b27ebb
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.dnf.FunctionalDependency;
+import tools.refinery.store.representation.AnySymbol;
+import tools.refinery.store.query.Constraint;
+
+import java.util.Set;
+
+public sealed interface AnySymbolView extends Constraint permits SymbolView {
+        AnySymbol getSymbol();
+
+        String getViewName();
+
+        default Set<FunctionalDependency<Integer>> getFunctionalDependencies() {
+                return Set.of();
+        }
+
+        default Set<ViewImplication> getImpliedRelationViews() {
+                return Set.of();
+        }
+
+        boolean get(Model model, Object[] tuple);
+
+        Iterable<Object[]> getAll(Model model);
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java
new file mode 100644
index 00000000..abae6e5c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java
@@ -0,0 +1,73 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.Objects;
+import java.util.function.BiPredicate;
+import java.util.function.Predicate;
+
+public class FilteredView<T> extends TuplePreservingView<T> {
+        private final BiPredicate<Tuple, T> predicate;
+
+        public FilteredView(Symbol<T> symbol, String name, BiPredicate<Tuple, T> predicate) {
+                super(symbol, name);
+                this.predicate = predicate;
+        }
+
+        public FilteredView(Symbol<T> symbol, BiPredicate<Tuple, T> predicate) {
+                super(symbol);
+                this.predicate = predicate;
+        }
+
+        public FilteredView(Symbol<T> symbol, String name, Predicate<T> predicate) {
+                this(symbol, name, (k, v) -> predicate.test(v));
+                validateDefaultValue(predicate);
+        }
+
+        public FilteredView(Symbol<T> symbol, Predicate<T> predicate) {
+                this(symbol, (k, v) -> predicate.test(v));
+                validateDefaultValue(predicate);
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, T value) {
+                return this.predicate.test(key, value);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                FilteredView<?> that = (FilteredView<?>) o;
+                return Objects.equals(predicate, that.predicate);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), predicate);
+        }
+
+        private void validateDefaultValue(Predicate<T> predicate) {
+                var defaultValue = getSymbol().defaultValue();
+                boolean matchesDefaultValue = false;
+                try {
+                        matchesDefaultValue = predicate.test(defaultValue);
+                } catch (NullPointerException e) {
+                        if (defaultValue != null) {
+                                throw e;
+                        }
+                        // The predicate doesn't need to handle the default value if it is null.
+                }
+                if (matchesDefaultValue) {
+                        throw new IllegalArgumentException("Tuples with default value %s cannot be enumerated in %s"
+                                        .formatted(defaultValue, getSymbol()));
+                }
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java
new file mode 100644
index 00000000..c312330e
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.tuple.Tuple;
+
+public class ForbiddenView extends TuplePreservingView<TruthValue> {
+        public ForbiddenView(Symbol<TruthValue> symbol) {
+                super(symbol, "forbidden");
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, TruthValue value) {
+                return !value.may();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java
new file mode 100644
index 00000000..74a5be07
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java
@@ -0,0 +1,36 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.query.term.*;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public final class FunctionView<T> extends AbstractFunctionView<T> {
+        public FunctionView(Symbol<T> symbol, String name) {
+                super(symbol, name, new Parameter(symbol.valueType(), ParameterDirection.OUT));
+        }
+
+        public FunctionView(Symbol<T> symbol) {
+                this(symbol, "function");
+        }
+
+        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, List<NodeVariable> arguments) {
+                return targetVariable -> {
+                        var placeholderVariable = Variable.of(getSymbol().valueType());
+                        var argumentsWithPlaceholder = new ArrayList<Variable>(arguments.size() + 1);
+                        argumentsWithPlaceholder.addAll(arguments);
+                        argumentsWithPlaceholder.add(placeholderVariable);
+                        return aggregateBy(placeholderVariable, aggregator, argumentsWithPlaceholder).toLiteral(targetVariable);
+                };
+        }
+
+        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, NodeVariable... arguments) {
+                return aggregate(aggregator, List.of(arguments));
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/KeyOnlyRelationView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/KeyOnlyView.java
index e1b2e45b..f0e4a61e 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/KeyOnlyRelationView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/KeyOnlyView.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.query.view;
 
 import tools.refinery.store.representation.Symbol;
@@ -5,19 +10,19 @@ import tools.refinery.store.tuple.Tuple;
 
 import java.util.Objects;
 
-public final class KeyOnlyRelationView<T> extends TuplePreservingRelationView<T> {
+public final class KeyOnlyView<T> extends TuplePreservingView<T> {
         public static final String VIEW_NAME = "key";
 
         private final T defaultValue;
 
-        public KeyOnlyRelationView(Symbol<T> symbol) {
+        public KeyOnlyView(Symbol<T> symbol) {
                 super(symbol, VIEW_NAME);
                 defaultValue = symbol.defaultValue();
         }
 
         @Override
-        public boolean filter(Tuple key, T value) {
-                return !Objects.equals(value, defaultValue);
+        protected boolean doFilter(Tuple key, T value) {
+                return true;
         }
 
         @Override
@@ -25,7 +30,7 @@ public final class KeyOnlyRelationView<T> extends TuplePreservingRelationView<T>
                 if (this == o) return true;
                 if (o == null || getClass() != o.getClass()) return false;
                 if (!super.equals(o)) return false;
-                KeyOnlyRelationView<?> that = (KeyOnlyRelationView<?>) o;
+                KeyOnlyView<?> that = (KeyOnlyView<?>) o;
                 return Objects.equals(defaultValue, that.defaultValue);
         }
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java
new file mode 100644
index 00000000..c322e220
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.tuple.Tuple;
+
+public class MayView extends TuplePreservingView<TruthValue> {
+        public MayView(Symbol<TruthValue> symbol) {
+                super(symbol, "may");
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, TruthValue value) {
+                return value.may();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java
new file mode 100644
index 00000000..65bb4e4c
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.tuple.Tuple;
+
+public class MustView extends TuplePreservingView<TruthValue> {
+        public MustView(Symbol<TruthValue> symbol) {
+                super(symbol, "must");
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, TruthValue value) {
+                return value.must();
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
new file mode 100644
index 00000000..fcf11506
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
@@ -0,0 +1,20 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple1;
+
+public final class NodeFunctionView extends AbstractFunctionView<Tuple1> {
+        public NodeFunctionView(Symbol<Tuple1> symbol, String name) {
+                super(symbol, name, Parameter.NODE_OUT);
+        }
+
+        public NodeFunctionView(Symbol<Tuple1> symbol) {
+                this(symbol, "function");
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/SymbolView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/SymbolView.java
new file mode 100644
index 00000000..cd8bd56b
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/SymbolView.java
@@ -0,0 +1,85 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.map.CursorAsIterator;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Objects;
+import java.util.UUID;
+
+/**
+ * Represents a view of a {@link Symbol} that can be queried.
+ *
+ * @param <T>
+ * @author Oszkar Semerath
+ */
+public abstract non-sealed class SymbolView<T> implements AnySymbolView {
+        private final Symbol<T> symbol;
+        private final String viewName;
+
+        protected SymbolView(Symbol<T> symbol, String viewName) {
+                this.symbol = symbol;
+                this.viewName = viewName;
+        }
+
+        protected SymbolView(Symbol<T> representation) {
+                this(representation, UUID.randomUUID().toString());
+        }
+
+        @Override
+        public Symbol<T> getSymbol() {
+                return symbol;
+        }
+
+        @Override
+        public String getViewName() {
+                return viewName;
+        }
+
+        @Override
+        public String name() {
+                return symbol.name() + "#" + viewName;
+        }
+
+        public final boolean filter(Tuple key, T value) {
+                return !Objects.equals(symbol.defaultValue(), value) && doFilter(key, value);
+        }
+
+        protected abstract boolean doFilter(Tuple key, T value);
+
+        public abstract Object[] forwardMap(Tuple key, T value);
+
+        @Override
+        public Iterable<Object[]> getAll(Model model) {
+                return (() -> new CursorAsIterator<>(model.getInterpretation(symbol).getAll(), this::forwardMap, this::filter));
+        }
+
+        @Override
+        public String toString() {
+                return name();
+        }
+
+        @Override
+        public String toReferenceString() {
+                return "@RelationView(\"%s\") %s".formatted(viewName, symbol.name());
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                SymbolView<?> that = (SymbolView<?>) o;
+                return Objects.equals(symbol, that.symbol) && Objects.equals(viewName, that.viewName);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(getClass(), symbol, viewName);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
new file mode 100644
index 00000000..6bc5a708
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
@@ -0,0 +1,82 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+
+public abstract class TuplePreservingView<T> extends SymbolView<T> {
+        private final List<Parameter> parameters;
+
+        protected TuplePreservingView(Symbol<T> symbol, String name) {
+                super(symbol, name);
+                this.parameters = createParameters(symbol.arity());
+        }
+
+        protected TuplePreservingView(Symbol<T> symbol) {
+                super(symbol);
+                this.parameters = createParameters(symbol.arity());
+        }
+
+        public Object[] forwardMap(Tuple key) {
+                Object[] result = new Object[key.getSize()];
+                for (int i = 0; i < key.getSize(); i++) {
+                        result[i] = Tuple.of(key.get(i));
+                }
+                return result;
+        }
+
+        @Override
+        public Object[] forwardMap(Tuple key, T value) {
+                return forwardMap(key);
+        }
+
+        @Override
+        public boolean get(Model model, Object[] tuple) {
+                int[] content = new int[tuple.length];
+                for (int i = 0; i < tuple.length; i++) {
+                        if (!(tuple[i] instanceof Tuple1 wrapper)) {
+                                return false;
+                        }
+                        content[i] = wrapper.value0();
+                }
+                Tuple key = Tuple.of(content);
+                T value = model.getInterpretation(getSymbol()).get(key);
+                return filter(key, value);
+        }
+
+        @Override
+        public List<Parameter> getParameters() {
+                return parameters;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                TuplePreservingView<?> that = (TuplePreservingView<?>) o;
+                return Objects.equals(parameters, that.parameters);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), parameters);
+        }
+
+        private static List<Parameter> createParameters(int arity) {
+                var parameters = new Parameter[arity];
+                Arrays.fill(parameters, Parameter.NODE_OUT);
+                return List.of(parameters);
+        }
+}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ViewImplication.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ViewImplication.java
new file mode 100644
index 00000000..fc2db9f2
--- /dev/null
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ViewImplication.java
@@ -0,0 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.view;
+
+import java.util.List;
+
+public record ViewImplication(AnySymbolView implyingView, AnySymbolView impliedView, List<Integer> impliedIndices) {
+        public ViewImplication {
+                if (impliedIndices.size() != impliedView.arity()) {
+                        throw new IllegalArgumentException("Expected %d implied indices for %s, but %d are provided"
+                                        .formatted(impliedView.arity(), impliedView, impliedIndices.size()));
+                }
+                for (var index : impliedIndices) {
+                        if (impliedView.invalidIndex(index)) {
+                                throw new IllegalArgumentException("%d is not a valid index for %s".formatted(index,
+                                                implyingView));
+                        }
+                }
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java
new file mode 100644
index 00000000..e17496e3
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java
@@ -0,0 +1,210 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+import tools.refinery.store.query.literal.BooleanLiteral;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.term.bool.BoolTerms;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.query.view.SymbolView;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static tools.refinery.store.query.literal.Literals.assume;
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
+
+class DnfBuilderLiteralEliminationTest {
+        private final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private final SymbolView<Boolean> friendView = new KeyOnlyView<>(friend);
+        private final NodeVariable p = Variable.of("p");
+        private final NodeVariable q = Variable.of("q");
+        private final Dnf trueDnf = Dnf.builder().parameter(p, ParameterDirection.IN).clause().build();
+        private final Dnf falseDnf = Dnf.builder().parameter(p).build();
+
+        @Test
+        void eliminateTrueTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(BooleanLiteral.TRUE, friendView.call(p, q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateTrueAssumptionTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(assume(BoolTerms.constant(true)), friendView.call(p, q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateFalseTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p), BooleanLiteral.FALSE)
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @ParameterizedTest
+        @CsvSource(value = {
+                        "false",
+                        "null"
+        }, nullValues = "null")
+        void eliminateFalseAssumptionTest(Boolean value) {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p), assume(BoolTerms.constant(value)))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysTrueTest() {
+                var actual = Dnf.builder()
+                                .parameters(List.of(p, q), ParameterDirection.IN)
+                                .clause(friendView.call(p, q))
+                                .clause(BooleanLiteral.TRUE)
+                                .build();
+                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysFalseTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q), BooleanLiteral.FALSE)
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateTrueDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(trueDnf.call(q), friendView.call(p, q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateFalseDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p), falseDnf.call(q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysTrueDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(List.of(p, q), ParameterDirection.IN)
+                                .clause(friendView.call(p, q))
+                                .clause(trueDnf.call(q))
+                                .build();
+                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysFalseDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q), falseDnf.call(q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateNotFalseDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(not(falseDnf.call(q)), friendView.call(p, q))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void eliminateNotTrueDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p), not(trueDnf.call(q)))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysNotFalseDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(List.of(p, q), ParameterDirection.IN)
+                                .clause(friendView.call(p, q))
+                                .clause(not(falseDnf.call(q)))
+                                .build();
+                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void alwaysNotTrueDnfTest() {
+                var actual = Dnf.builder()
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q), not(trueDnf.call(q)))
+                                .build();
+                var expected = Dnf.builder().parameters(p, q).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void removeDuplicateTest() {
+                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
+                                friendView.call(p, q),
+                                friendView.call(p, q)
+                )));
+                var expected = Dnf.of(builder -> builder.clause((p, q) -> List.of(friendView.call(p, q))));
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java
new file mode 100644
index 00000000..fc40c7b3
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java
@@ -0,0 +1,325 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.query.view.SymbolView;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
+
+class DnfBuilderVariableUnificationTest {
+        private final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private final Symbol<Boolean> children = Symbol.of("children", 2);
+        private final SymbolView<Boolean> friendView = new KeyOnlyView<>(friend);
+        private final SymbolView<Boolean> childrenView = new KeyOnlyView<>(children);
+
+        @Test
+        void equalToParameterTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        builder.clause(q -> List.of(
+                                        friendView.call(p, q),
+                                        p.isEquivalent(q)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(new SymbolicParameter(expectedP, ParameterDirection.OUT)),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void equalToParameterReverseTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        builder.clause(q -> List.of(
+                                        friendView.call(p, q),
+                                        q.isEquivalent(p)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(new SymbolicParameter(expectedP, ParameterDirection.OUT)),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void equalQuantifiedTest() {
+                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
+                                friendView.call(p, q),
+                                p.isEquivalent(q)
+                )));
+
+                var expectedP = Variable.of("p");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void equalQuantifiedTransitiveTest() {
+                var actual = Dnf.of(builder -> builder.clause((p, q, r) -> List.of(
+                                friendView.call(p, q),
+                                p.isEquivalent(q),
+                                childrenView.call(p, r),
+                                q.isEquivalent(r)
+                )));
+
+                var expectedP = Variable.of("p");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP), childrenView.call(expectedP, expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void equalQuantifiedTransitiveRemoveDuplicateTest() {
+                var actual = Dnf.of(builder -> builder.clause((p, q, r) -> List.of(
+                                friendView.call(p, q),
+                                p.isEquivalent(q),
+                                friendView.call(p, r),
+                                q.isEquivalent(r)
+                )));
+
+                var expectedP = Variable.of("p");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void parametersEqualTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause(
+                                        friendView.call(p, q),
+                                        p.isEquivalent(q)
+                        );
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(friendView.call(expectedP, expectedP), expectedQ.isEquivalent(expectedP))
+                                )
+                ));
+        }
+
+        @Test
+        void parametersEqualTransitiveTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        var r = builder.parameter("r");
+                        builder.clause(
+                                        friendView.call(p, q),
+                                        childrenView.call(p, r),
+                                        p.isEquivalent(q),
+                                        r.isEquivalent(q)
+                        );
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                var expectedR = Variable.of("r");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedR, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                expectedR.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void parameterAndQuantifiedEqualsTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause((r) -> List.of(
+                                        friendView.call(p, r),
+                                        p.isEquivalent(r),
+                                        childrenView.call(q, r),
+                                        q.isEquivalent(r)
+                        ));
+                });
+
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void parameterAndQuantifiedEqualsReverseFirstTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause((r) -> List.of(
+                                        friendView.call(p, r),
+                                        r.isEquivalent(p),
+                                        childrenView.call(q, r),
+                                        q.isEquivalent(r)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void parameterAndQuantifiedEqualsReverseSecondTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause((r) -> List.of(
+                                        friendView.call(p, r),
+                                        p.isEquivalent(r),
+                                        childrenView.call(q, r),
+                                        r.isEquivalent(q)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void parameterAndQuantifiedEqualsReverseBoth() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause((r) -> List.of(
+                                        friendView.call(p, r),
+                                        p.isEquivalent(r),
+                                        childrenView.call(q, r),
+                                        r.isEquivalent(q)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void parameterAndTwoQuantifiedEqualsTest() {
+                var actual = Dnf.of(builder -> {
+                        var p = builder.parameter("p");
+                        var q = builder.parameter("q");
+                        builder.clause((r, s) -> List.of(
+                                        r.isEquivalent(s),
+                                        friendView.call(p, r),
+                                        p.isEquivalent(r),
+                                        childrenView.call(q, s),
+                                        q.isEquivalent(s)
+                        ));
+                });
+
+                var expectedP = Variable.of("p");
+                var expectedQ = Variable.of("q");
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
+                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(expectedP, expectedP),
+                                                                expectedQ.isEquivalent(expectedP),
+                                                                childrenView.call(expectedP, expectedP)
+                                                )
+                                )
+                ));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java
new file mode 100644
index 00000000..d75d7f17
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java
@@ -0,0 +1,157 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static tools.refinery.store.query.literal.Literals.not;
+
+class DnfToDefinitionStringTest {
+        private static final Symbol<Boolean> person = Symbol.of("person", 1);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+
+        @Test
+        void noClausesTest() {
+                var dnf = Dnf.builder("Example").parameter(p).build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    <no clauses>.
+                                """));
+        }
+
+        @Test
+        void noParametersTest() {
+                var dnf = Dnf.builder("Example").build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example() <->
+                                    <no clauses>.
+                                """));
+        }
+
+        @Test
+        void emptyClauseTest() {
+                var dnf = Dnf.builder("Example").parameter(p, ParameterDirection.IN).clause().build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(@In p) <->
+                                    <empty>.
+                                """));
+        }
+
+        @Test
+        void relationViewPositiveTest() {
+                var dnf = Dnf.builder("Example").parameter(p).clause(friendView.call(p, q)).build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    @RelationView("key") friend(p, q).
+                                """));
+        }
+
+        @Test
+        void relationViewNegativeTest() {
+                var dnf = Dnf.builder("Example")
+                                .parameter(p, ParameterDirection.IN)
+                                .clause(not(friendView.call(p, q)))
+                                .build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(@In p) <->
+                                    !(@RelationView("key") friend(p, q)).
+                                """));
+        }
+
+        @Test
+        void relationViewTransitiveTest() {
+                var dnf = Dnf.builder("Example").parameter(p).clause(friendView.callTransitive(p, q)).build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    @RelationView("key") friend+(p, q).
+                                """));
+        }
+
+        @Test
+        void multipleParametersTest() {
+                var dnf = Dnf.builder("Example").parameters(p, q).clause(friendView.call(p, q)).build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p, q) <->
+                                    @RelationView("key") friend(p, q).
+                                """));
+        }
+
+        @Test
+        void multipleLiteralsTest() {
+                var dnf = Dnf.builder("Example")
+                                .parameter(p)
+                                .clause(
+                                                personView.call(p),
+                                                personView.call(q),
+                                                friendView.call(p, q)
+                                )
+                                .build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    @RelationView("key") person(p),
+                                    @RelationView("key") person(q),
+                                    @RelationView("key") friend(p, q).
+                                """));
+        }
+
+        @Test
+        void multipleClausesTest() {
+                var dnf = Dnf.builder("Example")
+                                .parameter(p)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p))
+                                .build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    @RelationView("key") friend(p, q)
+                                ;
+                                    @RelationView("key") friend(q, p).
+                                """));
+        }
+
+        @Test
+        void dnfTest() {
+                var r = Variable.of("r");
+                var s = Variable.of("s");
+                var called  = Dnf.builder("Called").parameters(r, s).clause(friendView.call(r, s)).build();
+                var dnf = Dnf.builder("Example")
+                                .parameter(p)
+                                .clause(
+                                                personView.call(p),
+                                                personView.call(q),
+                                                not(called.call(p, q))
+                                )
+                                .build();
+
+                assertThat(dnf.toDefinitionString(), is("""
+                                pred Example(p) <->
+                                    @RelationView("key") person(p),
+                                    @RelationView("key") person(q),
+                                    !(@Dnf Called(p, q)).
+                                """));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java
new file mode 100644
index 00000000..e22dbb21
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java
@@ -0,0 +1,112 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
+
+class TopologicalSortTest {
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final Dnf example = Dnf.of("example", builder -> {
+                var a = builder.parameter("a", ParameterDirection.IN);
+                var b = builder.parameter("b", ParameterDirection.IN);
+                var c = builder.parameter("c", ParameterDirection.OUT);
+                var d = builder.parameter("d", ParameterDirection.OUT);
+                builder.clause(
+                                friendView.call(a, b),
+                                friendView.call(b, c),
+                                friendView.call(c, d)
+                );
+        });
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+        private static final NodeVariable r = Variable.of("r");
+        private static final NodeVariable s = Variable.of("s");
+        private static final NodeVariable t = Variable.of("t");
+
+        @Test
+        void topologicalSortTest() {
+                var actual = Dnf.builder("Actual")
+                                .parameter(p, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(
+                                                not(friendView.call(p, q)),
+                                                example.call(p, q, r, s),
+                                                example.call(r, t, q, s),
+                                                friendView.call(r, t)
+                                )
+                                .build();
+
+                assertThat(actual, structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(p, ParameterDirection.IN),
+                                                new SymbolicParameter(q, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(
+                                                                friendView.call(r, t),
+                                                                example.call(r, t, q, s),
+                                                                not(friendView.call(p, q)),
+                                                                example.call(p, q, r, s)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void missingInputTest() {
+                var builder = Dnf.builder("Actual")
+                                .parameter(p, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(
+                                                not(friendView.call(p, q)),
+                                                example.call(p, q, r, s),
+                                                example.call(r, t, q, s),
+                                                friendView.call(r, t)
+                                );
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @Test
+        void missingVariableTest() {
+                var builder = Dnf.builder("Actual")
+                                .parameter(p, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(
+                                                not(friendView.call(p, q)),
+                                                example.call(p, q, r, s),
+                                                example.call(r, t, q, s)
+                                );
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @Test
+        void circularDependencyTest() {
+                var builder = Dnf.builder("Actual")
+                                .parameter(p, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(
+                                                not(friendView.call(p, q)),
+                                                example.call(p, q, r, s),
+                                                example.call(r, t, q, s),
+                                                example.call(p, q, r, t)
+                                );
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java
new file mode 100644
index 00000000..c52d26b2
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java
@@ -0,0 +1,428 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.dnf;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import tools.refinery.store.query.literal.BooleanLiteral;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.DataVariable;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.FunctionView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.hasItem;
+import static org.hamcrest.Matchers.not;
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.literal.Literals.assume;
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.term.int_.IntTerms.*;
+
+class VariableDirectionTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final Symbol<Integer> age = Symbol.of("age", 1, Integer.class);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final FunctionView<Integer> ageView = new FunctionView<>(age);
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+        private static final DataVariable<Integer> x = Variable.of("x", Integer.class);
+        private static final DataVariable<Integer> y = Variable.of("y", Integer.class);
+        private static final DataVariable<Integer> z = Variable.of("z", Integer.class);
+
+        @ParameterizedTest
+        @MethodSource("clausesWithVariableInput")
+        void unboundOutVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().parameter(p, ParameterDirection.OUT).clause(clause);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesWithVariableInput")
+        void unboundInVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().parameter(p, ParameterDirection.IN).clause(clause);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), hasItem(p));
+                }
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesWithVariableInput")
+        void boundPrivateVariableTest(List<? extends Literal> clause) {
+                var clauseWithBinding = new ArrayList<Literal>(clause);
+                clauseWithBinding.add(personView.call(p));
+                var builder = Dnf.builder().clause(clauseWithBinding);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), hasItem(p));
+                }
+        }
+
+        static Stream<Arguments> clausesWithVariableInput() {
+                return Stream.concat(
+                                clausesNotBindingVariable(),
+                                literalToClauseArgumentStream(literalsWithRequiredVariableInput())
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesNotBindingVariable")
+        void unboundPrivateVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().clause(clause);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), not(hasItem(p)));
+                }
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesNotBindingVariable")
+        void unboundByEquivalencePrivateVariableTest(List<? extends Literal> clause) {
+                var r = Variable.of("r");
+                var clauseWithEquivalence = new ArrayList<Literal>(clause);
+                clauseWithEquivalence.add(r.isEquivalent(p));
+                var builder = Dnf.builder().clause(clauseWithEquivalence);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        static Stream<Arguments> clausesNotBindingVariable() {
+                return Stream.concat(
+                                Stream.of(
+                                        Arguments.of(List.of()),
+                                        Arguments.of(List.of(BooleanLiteral.TRUE)),
+                                        Arguments.of(List.of(BooleanLiteral.FALSE))
+                                ),
+                                literalToClauseArgumentStream(literalsWithPrivateVariable())
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithPrivateVariable")
+        void unboundTwicePrivateVariableTest(Literal literal) {
+                var builder = Dnf.builder().clause(not(personView.call(p)), literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithPrivateVariable")
+        void unboundTwiceByEquivalencePrivateVariableTest(Literal literal) {
+                var r = Variable.of("r");
+                var builder = Dnf.builder().clause(not(personView.call(r)), r.isEquivalent(p), literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        static Stream<Arguments> literalsWithPrivateVariable() {
+                var dnfWithOutput = Dnf.builder("WithOutput")
+                                .parameter(p, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(friendView.call(p, q))
+                                .build();
+                var dnfWithOutputToAggregate = Dnf.builder("WithOutputToAggregate")
+                                .parameter(p, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .parameter(x, ParameterDirection.OUT)
+                                .clause(
+                                                friendView.call(p, q),
+                                                ageView.call(q, x)
+                                )
+                                .build();
+
+                return Stream.of(
+                                Arguments.of(not(friendView.call(p, q))),
+                                Arguments.of(y.assign(friendView.count(p, q))),
+                                Arguments.of(y.assign(ageView.aggregate(INT_SUM, p))),
+                                Arguments.of(not(dnfWithOutput.call(p, q))),
+                                Arguments.of(y.assign(dnfWithOutput.count(p, q))),
+                                Arguments.of(y.assign(dnfWithOutputToAggregate.aggregateBy(z, INT_SUM, p, q, z)))
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithRequiredVariableInput")
+        void unboundPrivateVariableTest(Literal literal) {
+                var builder = Dnf.builder().clause(literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithRequiredVariableInput")
+        void boundPrivateVariableInputTest(Literal literal) {
+                var builder = Dnf.builder().clause(personView.call(p), literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
+        }
+
+        static Stream<Arguments> literalsWithRequiredVariableInput() {
+                var dnfWithInput = Dnf.builder("WithInput")
+                                .parameter(p, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(friendView.call(p, q)).build();
+                var dnfWithInputToAggregate = Dnf.builder("WithInputToAggregate")
+                                .parameter(p, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .parameter(x, ParameterDirection.OUT)
+                                .clause(
+                                                friendView.call(p, q),
+                                                ageView.call(q, x)
+                                ).build();
+
+                return Stream.of(
+                                Arguments.of(dnfWithInput.call(p, q)),
+                                Arguments.of(dnfWithInput.call(p, p)),
+                                Arguments.of(not(dnfWithInput.call(p, q))),
+                                Arguments.of(not(dnfWithInput.call(p, p))),
+                                Arguments.of(y.assign(dnfWithInput.count(p, q))),
+                                Arguments.of(y.assign(dnfWithInput.count(p, p))),
+                                Arguments.of(y.assign(dnfWithInputToAggregate.aggregateBy(z, INT_SUM, p, q, z))),
+                                Arguments.of(y.assign(dnfWithInputToAggregate.aggregateBy(z, INT_SUM, p, p, z)))
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithVariableOutput")
+        void boundParameterTest(Literal literal) {
+                var builder = Dnf.builder().parameter(p, ParameterDirection.OUT).clause(literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithVariableOutput")
+        void boundTwiceParameterTest(Literal literal) {
+                var builder = Dnf.builder().parameter(p, ParameterDirection.IN).clause(literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithVariableOutput")
+        void boundPrivateVariableOutputTest(Literal literal) {
+                var dnfWithInput = Dnf.builder("WithInput")
+                                .parameter(p, ParameterDirection.IN)
+                                .clause(personView.call(p))
+                                .build();
+                var builder = Dnf.builder().clause(dnfWithInput.call(p), literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithVariableOutput")
+        void boundTwicePrivateVariableOutputTest(Literal literal) {
+                var builder = Dnf.builder().clause(personView.call(p), literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
+        }
+
+        static Stream<Arguments> literalsWithVariableOutput() {
+                var dnfWithOutput = Dnf.builder("WithOutput")
+                                .parameter(p, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(friendView.call(p, q))
+                                .build();
+
+                return Stream.of(
+                                Arguments.of(friendView.call(p, q)),
+                                Arguments.of(dnfWithOutput.call(p, q))
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesWithDataVariableInput")
+        void unboundOutDataVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().parameter(x, ParameterDirection.OUT).clause(clause);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesWithDataVariableInput")
+        void unboundInDataVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().parameter(x, ParameterDirection.IN).clause(clause);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), hasItem(x));
+                }
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesWithDataVariableInput")
+        void boundPrivateDataVariableTest(List<? extends Literal> clause) {
+                var clauseWithBinding = new ArrayList<Literal>(clause);
+                clauseWithBinding.add(x.assign(constant(27)));
+                var builder = Dnf.builder().clause(clauseWithBinding);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), hasItem(x));
+                }
+        }
+
+        static Stream<Arguments> clausesWithDataVariableInput() {
+                return Stream.concat(
+                                clausesNotBindingDataVariable(),
+                                literalToClauseArgumentStream(literalsWithRequiredDataVariableInput())
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("clausesNotBindingDataVariable")
+        void unboundPrivateDataVariableTest(List<? extends Literal> clause) {
+                var builder = Dnf.builder().clause(clause);
+                var dnf = assertDoesNotThrow(builder::build);
+                var clauses = dnf.getClauses();
+                if (clauses.size() > 0) {
+                        assertThat(clauses.get(0).positiveVariables(), not(hasItem(x)));
+                }
+        }
+
+        static Stream<Arguments> clausesNotBindingDataVariable() {
+                return Stream.concat(
+                                Stream.of(
+                                                Arguments.of(List.of()),
+                                                Arguments.of(List.of(BooleanLiteral.TRUE)),
+                                                Arguments.of(List.of(BooleanLiteral.FALSE))
+                                ),
+                                literalToClauseArgumentStream(literalsWithPrivateDataVariable())
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithPrivateDataVariable")
+        void unboundTwicePrivateDataVariableTest(Literal literal) {
+                var builder = Dnf.builder().clause(not(ageView.call(p, x)), literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        static Stream<Arguments> literalsWithPrivateDataVariable() {
+                var dnfWithOutput = Dnf.builder("WithDataOutput")
+                                .parameter(y, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(ageView.call(q, y))
+                                .build();
+
+                return Stream.of(
+                                Arguments.of(not(ageView.call(q, x))),
+                                Arguments.of(y.assign(ageView.count(q, x))),
+                                Arguments.of(not(dnfWithOutput.call(x, q)))
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithRequiredDataVariableInput")
+        void unboundPrivateDataVariableTest(Literal literal) {
+                var builder = Dnf.builder().clause(literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        static Stream<Arguments> literalsWithRequiredDataVariableInput() {
+                var dnfWithInput = Dnf.builder("WithDataInput")
+                                .parameter(y, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(ageView.call(q, x))
+                                .build();
+                // We are passing {@code y} to the parameter named {@code right} of {@code greaterEq}.
+                @SuppressWarnings("SuspiciousNameCombination")
+                var dnfWithInputToAggregate = Dnf.builder("WithDataInputToAggregate")
+                                .parameter(y, ParameterDirection.IN)
+                                .parameter(q, ParameterDirection.OUT)
+                                .parameter(x, ParameterDirection.OUT)
+                                .clause(
+                                                friendView.call(p, q),
+                                                ageView.call(q, x),
+                                                assume(greaterEq(x, y))
+                                )
+                                .build();
+
+                return Stream.of(
+                                Arguments.of(dnfWithInput.call(x, q)),
+                                Arguments.of(not(dnfWithInput.call(x, q))),
+                                Arguments.of(y.assign(dnfWithInput.count(x, q))),
+                                Arguments.of(y.assign(dnfWithInputToAggregate.aggregateBy(z, INT_SUM, x, q, z)))
+                );
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithDataVariableOutput")
+        void boundDataParameterTest(Literal literal) {
+                var builder = Dnf.builder().parameter(x, ParameterDirection.OUT).clause(literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(x));
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithDataVariableOutput")
+        void boundTwiceDataParameterTest(Literal literal) {
+                var builder = Dnf.builder().parameter(x, ParameterDirection.IN).clause(literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithDataVariableOutput")
+        void boundPrivateDataVariableOutputTest(Literal literal) {
+                var dnfWithInput = Dnf.builder("WithInput")
+                                .parameter(x, ParameterDirection.IN)
+                                .clause(assume(greaterEq(x, constant(24))))
+                                .build();
+                var builder = Dnf.builder().clause(dnfWithInput.call(x), literal);
+                var dnf = assertDoesNotThrow(builder::build);
+                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(x));
+        }
+
+        @ParameterizedTest
+        @MethodSource("literalsWithDataVariableOutput")
+        void boundTwicePrivateDataVariableOutputTest(Literal literal) {
+                var builder = Dnf.builder().clause(x.assign(constant(27)), literal);
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        static Stream<Arguments> literalsWithDataVariableOutput() {
+                var dnfWithOutput = Dnf.builder("WithOutput")
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(personView.call(q))
+                                .build();
+                var dnfWithDataOutput = Dnf.builder("WithDataOutput")
+                                .parameter(y, ParameterDirection.OUT)
+                                .parameter(q, ParameterDirection.OUT)
+                                .clause(ageView.call(q, y))
+                                .build();
+                var dnfWithOutputToAggregate = Dnf.builder("WithDataOutputToAggregate")
+                                .parameter(q, ParameterDirection.OUT)
+                                .parameter(y, ParameterDirection.OUT)
+                                .clause(ageView.call(q, y))
+                                .build();
+
+                return Stream.of(
+                                Arguments.of(x.assign(constant(24))),
+                                Arguments.of(ageView.call(q, x)),
+                                Arguments.of(x.assign(personView.count(q))),
+                                Arguments.of(x.assign(ageView.aggregate(INT_SUM, q))),
+                                Arguments.of(dnfWithDataOutput.call(x, q)),
+                                Arguments.of(x.assign(dnfWithOutput.count(q))),
+                                Arguments.of(x.assign(dnfWithOutputToAggregate.aggregateBy(z, INT_SUM, q, z)))
+                );
+        }
+
+        private static Stream<Arguments> literalToClauseArgumentStream(Stream<Arguments> literalArgumentsStream) {
+                return literalArgumentsStream.map(arguments -> Arguments.of(List.of(arguments.get()[0])));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java
new file mode 100644
index 00000000..35910e08
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java
@@ -0,0 +1,88 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.term.*;
+
+import java.util.List;
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.empty;
+import static org.junit.jupiter.api.Assertions.assertAll;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.literal.Literals.not;
+import static tools.refinery.store.query.term.int_.IntTerms.INT_SUM;
+import static tools.refinery.store.query.term.int_.IntTerms.constant;
+
+class AggregationLiteralTest {
+        private static final NodeVariable p = Variable.of("p");
+        private static final DataVariable<Integer> x = Variable.of("x", Integer.class);
+        private static final DataVariable<Integer> y = Variable.of("y", Integer.class);
+        private static final DataVariable<Integer> z = Variable.of("z", Integer.class);
+        private static final Constraint fakeConstraint = new Constraint() {
+                @Override
+                public String name() {
+                        return getClass().getName();
+                }
+
+                @Override
+                public List<Parameter> getParameters() {
+                        return List.of(
+                                        new Parameter(null, ParameterDirection.OUT),
+                                        new Parameter(Integer.class, ParameterDirection.OUT)
+                        );
+                }
+        };
+
+        @Test
+        void parameterDirectionTest() {
+                var literal = x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y));
+                assertAll(
+                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(x)),
+                                () -> assertThat(literal.getInputVariables(Set.of()), empty()),
+                                () -> assertThat(literal.getInputVariables(Set.of(p)), containsInAnyOrder(p)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(p, y)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of(p)), containsInAnyOrder(y))
+                );
+        }
+
+        @Test
+        void missingAggregationVariableTest() {
+                var aggregation = fakeConstraint.aggregateBy(y, INT_SUM, p, z);
+                assertThrows(IllegalArgumentException.class, () -> x.assign(aggregation));
+        }
+
+        @Test
+        void circularAggregationVariableTest() {
+                var aggregation = fakeConstraint.aggregateBy(x, INT_SUM, p, x);
+                assertThrows(IllegalArgumentException.class, () -> x.assign(aggregation));
+        }
+
+        @Test
+        void unboundTwiceVariableTest() {
+                var builder = Dnf.builder()
+                                .clause(
+                                                not(fakeConstraint.call(p, y)),
+                                                x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y))
+                                );
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+
+        @Test
+        void unboundBoundVariableTest() {
+                var builder = Dnf.builder()
+                                .clause(
+                                                y.assign(constant(27)),
+                                                x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y))
+                                );
+                assertThrows(IllegalArgumentException.class, builder::build);
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java
new file mode 100644
index 00000000..a01c6586
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java
@@ -0,0 +1,94 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.literal;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+
+import java.util.List;
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.empty;
+import static org.junit.jupiter.api.Assertions.assertAll;
+import static tools.refinery.store.query.literal.Literals.not;
+
+class CallLiteralTest {
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+        private static final NodeVariable r = Variable.of("r");
+        private static final NodeVariable s = Variable.of("s");
+
+        private static final Constraint fakeConstraint = new Constraint() {
+                @Override
+                public String name() {
+                        return getClass().getName();
+                }
+
+                @Override
+                public List<Parameter> getParameters() {
+                        return List.of(
+                                        new Parameter(null, ParameterDirection.IN),
+                                        new Parameter(null, ParameterDirection.IN),
+                                        new Parameter(null, ParameterDirection.OUT),
+                                        new Parameter(null, ParameterDirection.OUT)
+                        );
+                }
+        };
+
+        @Test
+        void notRepeatedPositiveDirectionTest() {
+                var literal = fakeConstraint.call(p, q, r, s);
+                assertAll(
+                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(r, s)),
+                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p, q)),
+                                () -> assertThat(literal.getInputVariables(Set.of(p, q, r)), containsInAnyOrder(p, q)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of()), empty()),
+                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q, r)), empty())
+                );
+        }
+
+        @Test
+        void notRepeatedNegativeDirectionTest() {
+                var literal = not(fakeConstraint.call(p, q, r, s));
+                assertAll(
+                                () -> assertThat(literal.getOutputVariables(), empty()),
+                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p, q)),
+                                () -> assertThat(literal.getInputVariables(Set.of(p, q, r)), containsInAnyOrder(p, q, r)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(r, s)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q, r)), containsInAnyOrder(s))
+                );
+        }
+
+        @Test
+        void repeatedPositiveDirectionTest() {
+                var literal = fakeConstraint.call(p, p, q, q);
+                assertAll(
+                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(q)),
+                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p)),
+                                () -> assertThat(literal.getInputVariables(Set.of(p, q)), containsInAnyOrder(p)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of()), empty()),
+                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q)), empty())
+                );
+        }
+
+        @Test
+        void repeatedNegativeDirectionTest() {
+                var literal = not(fakeConstraint.call(p, p, q, q));
+                assertAll(
+                                () -> assertThat(literal.getOutputVariables(), empty()),
+                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p)),
+                                () -> assertThat(literal.getInputVariables(Set.of(p, q)), containsInAnyOrder(p, q)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(q)),
+                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q)), empty())
+                );
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java
new file mode 100644
index 00000000..1cbc101a
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java
@@ -0,0 +1,97 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.query.term.bool.BoolTerms;
+import tools.refinery.store.query.term.int_.IntTerms;
+import tools.refinery.store.query.term.real.RealTerms;
+import tools.refinery.store.query.term.uppercardinality.UpperCardinalityTerms;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+import java.util.List;
+import java.util.stream.Stream;
+
+class TermSubstitutionTest {
+        private final static DataVariable<Integer> intA = Variable.of("intA", Integer.class);
+        private final static DataVariable<Integer> intB = Variable.of("intB", Integer.class);
+        private final static DataVariable<Double> realA = Variable.of("realA", Double.class);
+        private final static DataVariable<Double> realB = Variable.of("realB", Double.class);
+        private final static DataVariable<Boolean> boolA = Variable.of("boolA", Boolean.class);
+        private final static DataVariable<Boolean> boolB = Variable.of("boolB", Boolean.class);
+        private final static DataVariable<UpperCardinality> upperCardinalityA = Variable.of("upperCardinalityA",
+                        UpperCardinality.class);
+        private final static DataVariable<UpperCardinality> upperCardinalityB = Variable.of("upperCardinalityB",
+                        UpperCardinality.class);
+        private final static Substitution substitution = Substitution.builder()
+                        .put(intA, intB)
+                        .put(intB, intA)
+                        .put(realA, realB)
+                        .put(realB, realA)
+                        .put(boolA, boolB)
+                        .put(boolB, boolA)
+                        .put(upperCardinalityA, upperCardinalityB)
+                        .put(upperCardinalityB, upperCardinalityA)
+                        .build();
+
+        @ParameterizedTest
+        @MethodSource
+        void substitutionTest(AnyTerm term) {
+                var substitutedTerm1 = term.substitute(substitution);
+                Assertions.assertNotEquals(term, substitutedTerm1, "Original term is not equal to substituted term");
+                var helper = new LiteralEqualityHelper(Dnf::equals, List.of(), List.of());
+                Assertions.assertTrue(term.equalsWithSubstitution(helper, substitutedTerm1), "Terms are equal by helper");
+                // The {@link #substitution} is its own inverse.
+                var substitutedTerm2 = substitutedTerm1.substitute(substitution);
+                Assertions.assertEquals(term, substitutedTerm2, "Original term is not equal to back-substituted term");
+        }
+
+        static Stream<Arguments> substitutionTest() {
+                return Stream.of(
+                                Arguments.of(IntTerms.plus(intA)),
+                                Arguments.of(IntTerms.minus(intA)),
+                                Arguments.of(IntTerms.add(intA, intB)),
+                                Arguments.of(IntTerms.sub(intA, intB)),
+                                Arguments.of(IntTerms.mul(intA, intB)),
+                                Arguments.of(IntTerms.div(intA, intB)),
+                                Arguments.of(IntTerms.pow(intA, intB)),
+                                Arguments.of(IntTerms.min(intA, intB)),
+                                Arguments.of(IntTerms.max(intA, intB)),
+                                Arguments.of(IntTerms.eq(intA, intB)),
+                                Arguments.of(IntTerms.notEq(intA, intB)),
+                                Arguments.of(IntTerms.less(intA, intB)),
+                                Arguments.of(IntTerms.lessEq(intA, intB)),
+                                Arguments.of(IntTerms.greater(intA, intB)),
+                                Arguments.of(IntTerms.greaterEq(intA, intB)),
+                                Arguments.of(IntTerms.asInt(realA)),
+                                Arguments.of(RealTerms.plus(realA)),
+                                Arguments.of(RealTerms.minus(realA)),
+                                Arguments.of(RealTerms.add(realA, realB)),
+                                Arguments.of(RealTerms.sub(realA, realB)),
+                                Arguments.of(RealTerms.mul(realA, realB)),
+                                Arguments.of(RealTerms.div(realA, realB)),
+                                Arguments.of(RealTerms.pow(realA, realB)),
+                                Arguments.of(RealTerms.min(realA, realB)),
+                                Arguments.of(RealTerms.max(realA, realB)),
+                                Arguments.of(RealTerms.asReal(intA)),
+                                Arguments.of(BoolTerms.not(boolA)),
+                                Arguments.of(BoolTerms.and(boolA, boolB)),
+                                Arguments.of(BoolTerms.or(boolA, boolB)),
+                                Arguments.of(BoolTerms.xor(boolA, boolB)),
+                                Arguments.of(RealTerms.eq(realA, realB)),
+                                Arguments.of(UpperCardinalityTerms.add(upperCardinalityA, upperCardinalityB)),
+                                Arguments.of(UpperCardinalityTerms.mul(upperCardinalityA, upperCardinalityB)),
+                                Arguments.of(UpperCardinalityTerms.min(upperCardinalityA, upperCardinalityB)),
+                                Arguments.of(UpperCardinalityTerms.max(upperCardinalityA, upperCardinalityB))
+                );
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java
new file mode 100644
index 00000000..beff705e
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java
@@ -0,0 +1,75 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.bool;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+import tools.refinery.store.query.valuation.Valuation;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+
+class BoolTermsEvaluateTest {
+        @ParameterizedTest(name = "!{0} == {1}")
+        @CsvSource(value = {
+                        "false, true",
+                        "true, false",
+                        "null, null"
+        }, nullValues = "null")
+        void notTest(Boolean a, Boolean result) {
+                var term = BoolTerms.not(BoolTerms.constant(a));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} && {1} == {2}")
+        @CsvSource(value = {
+                        "false, false, false",
+                        "false, true, false",
+                        "true, false, false",
+                        "true, true, true",
+                        "false, null, null",
+                        "null, false, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void andTest(Boolean a, Boolean b, Boolean result) {
+                var term = BoolTerms.and(BoolTerms.constant(a), BoolTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} || {1} == {2}")
+        @CsvSource(value = {
+                        "false, false, false",
+                        "false, true, true",
+                        "true, false, true",
+                        "true, true, true",
+                        "true, null, null",
+                        "null, true, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void orTest(Boolean a, Boolean b, Boolean result) {
+                var term = BoolTerms.or(BoolTerms.constant(a), BoolTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} ^^ {1} == {2}")
+        @CsvSource(value = {
+                        "false, false, false",
+                        "false, true, true",
+                        "true, false, true",
+                        "true, true, false",
+                        "false, null, null",
+                        "null, false, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void xorTest(Boolean a, Boolean b, Boolean result) {
+                var term = BoolTerms.xor(BoolTerms.constant(a), BoolTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java
new file mode 100644
index 00000000..abe50d75
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java
@@ -0,0 +1,259 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.int_;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.CsvSource;
+import org.junit.jupiter.params.provider.MethodSource;
+import tools.refinery.store.query.term.real.RealTerms;
+import tools.refinery.store.query.valuation.Valuation;
+
+import java.util.stream.Stream;
+
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+class IntTermsEvaluateTest {
+        @ParameterizedTest(name = "+{0} == {1}")
+        @CsvSource(value = {
+                        "2, 2",
+                        "null, null"
+        }, nullValues = "null")
+        void plusTest(Integer a, Integer result) {
+                var term = IntTerms.plus(IntTerms.constant(a));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "-{0} == {1}")
+        @CsvSource(value = {
+                        "2, -2",
+                        "null, null"
+        }, nullValues = "null")
+        void minusTest(Integer a, Integer result) {
+                var term = IntTerms.minus(IntTerms.constant(a));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} + {1} == {2}")
+        @CsvSource(value = {
+                        "1, 2, 3",
+                        "null, 2, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void addTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.add(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} - {1} == {2}")
+        @CsvSource(value = {
+                        "1, 3, -2",
+                        "null, 3, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void subTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.sub(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} * {1} == {2}")
+        @CsvSource(value = {
+                        "2, 3, 6",
+                        "null, 3, null",
+                        "2, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void mulTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.mul(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} * {1} == {2}")
+        @CsvSource(value = {
+                        "6, 3, 2",
+                        "7, 3, 2",
+                        "6, 0, null",
+                        "null, 3, null",
+                        "6, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void divTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.div(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} ** {1} == {2}")
+        @CsvSource(value = {
+                        "1, 0, 1",
+                        "1, 3, 1",
+                        "1, -3, null",
+                        "2, 0, 1",
+                        "2, 2, 4",
+                        "2, 3, 8",
+                        "2, 4, 16",
+                        "2, 5, 32",
+                        "2, 6, 64",
+                        "2, -3, null",
+                        "null, 3, null",
+                        "2, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void powTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.pow(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "min({0}, {1}) == {2}")
+        @CsvSource(value = {
+                        "1, 2, 1",
+                        "2, 1, 1",
+                        "null, 2, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void minTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.min(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "max({0}, {1}) == {2}")
+        @CsvSource(value = {
+                        "1, 2, 2",
+                        "2, 1, 2",
+                        "null, 2, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void maxTest(Integer a, Integer b, Integer result) {
+                var term = IntTerms.max(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} == {1}) == {2}")
+        @CsvSource(value = {
+                        "1, 1, true",
+                        "1, 2, false",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void eqTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.eq(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} != {1}) == {2}")
+        @CsvSource(value = {
+                        "1, 1, false",
+                        "1, 2, true",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void notEqTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.notEq(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} < {1}) == {2}")
+        @CsvSource(value = {
+                        "1, -2, false",
+                        "1, 1, false",
+                        "1, 2, true",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void lessTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.less(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} <= {1}) == {2}")
+        @CsvSource(value = {
+                        "1, -2, false",
+                        "1, 1, true",
+                        "1, 2, true",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void lessEqTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.lessEq(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} > {1}) == {2}")
+        @CsvSource(value = {
+                        "1, -2, true",
+                        "1, 1, false",
+                        "1, 2, false",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void greaterTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.greater(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} >= {1}) == {2}")
+        @CsvSource(value = {
+                        "1, -2, true",
+                        "1, 1, true",
+                        "1, 2, false",
+                        "null, 1, null",
+                        "1, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void greaterEqTest(Integer a, Integer b, Boolean result) {
+                var term = IntTerms.greaterEq(IntTerms.constant(a), IntTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} as int == {1}")
+        @MethodSource
+        void asIntTest(Double a, Integer result) {
+                var term = IntTerms.asInt(RealTerms.constant(a));
+                assertThat(term.getType(), is(Integer.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        static Stream<Arguments> asIntTest() {
+                return Stream.of(
+                                Arguments.of(2.0, 2),
+                                Arguments.of(2.1, 2),
+                                Arguments.of(2.9, 2),
+                                Arguments.of(-2.0, -2),
+                                Arguments.of(-2.1, -2),
+                                Arguments.of(-2.9, -2),
+                                Arguments.of(0.0, 0),
+                                Arguments.of(-0.0, 0),
+                                Arguments.of(Double.POSITIVE_INFINITY, Integer.MAX_VALUE),
+                                Arguments.of(Double.NEGATIVE_INFINITY, Integer.MIN_VALUE),
+                                Arguments.of(Double.NaN, null),
+                                Arguments.of(null, null)
+                );
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java
new file mode 100644
index 00000000..6a8eebf1
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java
@@ -0,0 +1,238 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.real;
+
+import org.hamcrest.Matcher;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+import tools.refinery.store.query.term.int_.IntTerms;
+import tools.refinery.store.query.valuation.Valuation;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.*;
+
+class RealTermEvaluateTest {
+        public static final double TOLERANCE = 1e-6;
+
+        private static Matcher<Double> closeToOrNull(Double expected) {
+                return expected == null ? nullValue(Double.class) : closeTo(expected, TOLERANCE);
+        }
+
+        @ParameterizedTest(name = "+{0} == {1}")
+        @CsvSource(value = {
+                        "2.5, 2.5",
+                        "null, null"
+        }, nullValues = "null")
+        void plusTest(Double a, Double result) {
+                var term = RealTerms.plus(RealTerms.constant(a));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "-{0} == {1}")
+        @CsvSource(value = {
+                        "2.5, -2.5",
+                        "null, null"
+        }, nullValues = "null")
+        void minusTest(Double a, Double result) {
+                var term = RealTerms.minus(RealTerms.constant(a));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "{0} + {1} == {2}")
+        @CsvSource(value = {
+                        "1.2, 2.3, 3.5",
+                        "null, 2.3, null",
+                        "1.2, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void addTest(Double a, Double b, Double result) {
+                var term = RealTerms.add(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "{0} - {1} == {2}")
+        @CsvSource(value = {
+                        "1.2, 3.4, -2.2",
+                        "null, 3.4, null",
+                        "1.2, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void subTest(Double a, Double b, Double result) {
+                var term = RealTerms.sub(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "{0} * {1} == {2}")
+        @CsvSource(value = {
+                        "2.3, 3.4, 7.82",
+                        "null, 3.4, null",
+                        "2.3, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void mulTest(Double a, Double b, Double result) {
+                var term = RealTerms.mul(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "{0} * {1} == {2}")
+        @CsvSource(value = {
+                        "7.82, 3.4, 2.3",
+                        "null, 3.4, null",
+                        "7.82, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void divTest(Double a, Double b, Double result) {
+                var term = RealTerms.div(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "{0} ** {1} == {2}")
+        @CsvSource(value = {
+                        "2.0, 6.0, 64.0",
+                        "null, 6.0, null",
+                        "2.0, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void powTest(Double a, Double b, Double result) {
+                var term = RealTerms.pow(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "min({0}, {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, 2.7, 1.5",
+                        "2.7, 1.5, 1.5",
+                        "null, 2.7, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void minTest(Double a, Double b, Double result) {
+                var term = RealTerms.min(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "max({0}, {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, 2.7, 2.7",
+                        "2.7, 1.7, 2.7",
+                        "null, 2.7, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void maxTest(Double a, Double b, Double result) {
+                var term = RealTerms.max(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+
+        @ParameterizedTest(name = "({0} == {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, 1.5, true",
+                        "1.5, 2.7, false",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void eqTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.eq(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} != {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, 1.5, false",
+                        "1.5, 2.7, true",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void notEqTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.notEq(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} < {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, -2.7, false",
+                        "1.5, 1.5, false",
+                        "1.5, 2.7, true",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void lessTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.less(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} <= {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, -2.7, false",
+                        "1.5, 1.5, true",
+                        "1.5, 2.7, true",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void lessEqTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.lessEq(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} > {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, -2.7, true",
+                        "1.5, 1.5, false",
+                        "1.5, 2.7, false",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void greaterTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.greater(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "({0} >= {1}) == {2}")
+        @CsvSource(value = {
+                        "1.5, -2.7, true",
+                        "1.5, 1.5, true",
+                        "1.5, 2.7, false",
+                        "null, 1.5, null",
+                        "1.5, null, null",
+                        "null, null, null"
+        }, nullValues = "null")
+        void greaterEqTest(Double a, Double b, Boolean result) {
+                var term = RealTerms.greaterEq(RealTerms.constant(a), RealTerms.constant(b));
+                assertThat(term.getType(), is(Boolean.class));
+                assertThat(term.evaluate(Valuation.empty()), is(result));
+        }
+
+        @ParameterizedTest(name = "{0} as real == {1}")
+        @CsvSource(value = {
+                        "0, 0.0",
+                        "5, 5.0",
+                        "null, null"
+        }, nullValues = "null")
+        void asRealTest(Integer a, Double result) {
+                var term = RealTerms.asReal(IntTerms.constant(a));
+                assertThat(term.getType(), is(Double.class));
+                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
+        }
+}
diff --git a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperatorStreamTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorStreamTest.java
index c529117e..31baf36e 100644
--- a/subprojects/store-query-viatra/src/test/java/tools/refinery/store/query/viatra/internal/cardinality/UpperCardinalitySumAggregationOperatorStreamTest.java
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorStreamTest.java
@@ -1,4 +1,9 @@
-package tools.refinery.store.query.viatra.internal.cardinality;
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
 
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
@@ -10,14 +15,14 @@ import java.util.List;
 import java.util.stream.Stream;
 
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.is;
 
-class UpperCardinalitySumAggregationOperatorStreamTest {
+class UpperCardinalitySumAggregatorStreamTest {
         @ParameterizedTest
         @MethodSource
         void testStream(List<UpperCardinality> list, UpperCardinality expected) {
-                var result = UpperCardinalitySumAggregationOperator.INSTANCE.aggregateStream(list.stream());
-                assertThat(result, equalTo(expected));
+                var result = UpperCardinalitySumAggregator.INSTANCE.aggregateStream(list.stream());
+                assertThat(result, is(expected));
         }
 
         static Stream<Arguments> testStream() {
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java
new file mode 100644
index 00000000..780cd0ab
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java
@@ -0,0 +1,80 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.term.StatefulAggregate;
+import tools.refinery.store.representation.cardinality.UpperCardinalities;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+
+class UpperCardinalitySumAggregatorTest {
+        private StatefulAggregate<UpperCardinality, UpperCardinality> accumulator;
+
+        @BeforeEach
+        void beforeEach() {
+                accumulator = UpperCardinalitySumAggregator.INSTANCE.createEmptyAggregate();
+        }
+
+        @Test
+        void emptyAggregationTest() {
+                assertThat(accumulator.getResult(), is(UpperCardinality.of(0)));
+        }
+
+        @Test
+        void singleBoundedTest() {
+                accumulator.add(UpperCardinality.of(3));
+                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
+        }
+
+        @Test
+        void multipleBoundedTest() {
+                accumulator.add(UpperCardinality.of(2));
+                accumulator.add(UpperCardinality.of(3));
+                assertThat(accumulator.getResult(), is(UpperCardinality.of(5)));
+        }
+
+        @Test
+        void singleUnboundedTest() {
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
+        }
+
+        @Test
+        void multipleUnboundedTest() {
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
+        }
+
+        @Test
+        void removeBoundedTest() {
+                accumulator.add(UpperCardinality.of(2));
+                accumulator.add(UpperCardinality.of(3));
+                accumulator.remove(UpperCardinality.of(2));
+                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
+        }
+
+        @Test
+        void removeAllUnboundedTest() {
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                accumulator.add(UpperCardinality.of(3));
+                accumulator.remove(UpperCardinalities.UNBOUNDED);
+                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
+        }
+
+        @Test
+        void removeSomeUnboundedTest() {
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                accumulator.add(UpperCardinalities.UNBOUNDED);
+                accumulator.add(UpperCardinality.of(3));
+                accumulator.remove(UpperCardinalities.UNBOUNDED);
+                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java
new file mode 100644
index 00000000..9d0f3bde
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java
@@ -0,0 +1,104 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.term.uppercardinality;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import tools.refinery.store.query.valuation.Valuation;
+import tools.refinery.store.representation.cardinality.UpperCardinalities;
+import tools.refinery.store.representation.cardinality.UpperCardinality;
+
+import java.util.stream.Stream;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+
+class UpperCardinalityTermsEvaluateTest {
+        @ParameterizedTest(name = "min({0}, {1}) == {2}")
+        @MethodSource
+        void minTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
+                var term = UpperCardinalityTerms.min(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
+                assertThat(term.getType(), is(UpperCardinality.class));
+                assertThat(term.evaluate(Valuation.empty()), is(expected));
+        }
+
+        static Stream<Arguments> minTest() {
+                return Stream.of(
+                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(0), UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(1), UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinality.of(1), UpperCardinality.of(0), UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinality.of(0), UpperCardinalities.UNBOUNDED, UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(0), UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinality.of(1), null, null),
+                                Arguments.of(null, UpperCardinality.of(1), null),
+                                Arguments.of(null, null, null)
+                );
+        }
+
+        @ParameterizedTest(name = "max({0}, {1}) == {2}")
+        @MethodSource
+        void maxTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
+                var term = UpperCardinalityTerms.max(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
+                assertThat(term.getType(), is(UpperCardinality.class));
+                assertThat(term.evaluate(Valuation.empty()), is(expected));
+        }
+
+        static Stream<Arguments> maxTest() {
+                return Stream.of(
+                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(0), UpperCardinality.of(0)),
+                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(1), UpperCardinality.of(1)),
+                                Arguments.of(UpperCardinality.of(1), UpperCardinality.of(0), UpperCardinality.of(1)),
+                                Arguments.of(UpperCardinality.of(0), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(0), UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinality.of(1), null, null),
+                                Arguments.of(null, UpperCardinality.of(1), null),
+                                Arguments.of(null, null, null)
+                );
+        }
+
+        @ParameterizedTest(name = "{0} + {1} == {2}")
+        @MethodSource
+        void addTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
+                var term = UpperCardinalityTerms.add(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
+                assertThat(term.getType(), is(UpperCardinality.class));
+                assertThat(term.evaluate(Valuation.empty()), is(expected));
+        }
+
+        static Stream<Arguments> addTest() {
+                return Stream.of(
+                                Arguments.of(UpperCardinality.of(2), UpperCardinality.of(3), UpperCardinality.of(5)),
+                                Arguments.of(UpperCardinality.of(2), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(2), UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinality.of(1), null, null),
+                                Arguments.of(null, UpperCardinality.of(1), null),
+                                Arguments.of(null, null, null)
+                );
+        }
+
+        @ParameterizedTest(name = "{0} * {1} == {2}")
+        @MethodSource
+        void mulTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
+                var term = UpperCardinalityTerms.mul(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
+                assertThat(term.getType(), is(UpperCardinality.class));
+                assertThat(term.evaluate(Valuation.empty()), is(expected));
+        }
+
+        static Stream<Arguments> mulTest() {
+                return Stream.of(
+                                Arguments.of(UpperCardinality.of(2), UpperCardinality.of(3), UpperCardinality.of(6)),
+                                Arguments.of(UpperCardinality.of(2), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(2), UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
+                                Arguments.of(UpperCardinality.of(1), null, null),
+                                Arguments.of(null, UpperCardinality.of(1), null),
+                                Arguments.of(null, null, null)
+                );
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java
new file mode 100644
index 00000000..d447e99c
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java
@@ -0,0 +1,159 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.List;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.allOf;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
+
+class StructurallyEqualToRawTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+
+        @Test
+        void flatEqualsTest() {
+                var actual = Dnf.builder("Actual").parameters(p).clause(personView.call(p)).build();
+
+                assertThat(actual, structurallyEqualTo(
+                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
+                                List.of(List.of(personView.call(q)))
+                ));
+        }
+
+        @Test
+        void flatNotEqualsTest() {
+                var actual = Dnf.builder("Actual").parameters(p).clause(friendView.call(p, q)).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
+                                List.of(List.of(friendView.call(q, q)))
+                );
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void deepEqualsTest() {
+                var actual = Dnf.builder("Actual").parameters(q).clause(
+                                Dnf.builder("Actual2").parameters(p).clause(personView.call(p)).build().call(q)
+                ).build();
+
+                assertThat(actual, structurallyEqualTo(
+                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
+                                List.of(
+                                                List.of(
+                                                                Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build().call(q)
+                                                )
+                                )
+                ));
+        }
+
+        @Test
+        void deepNotEqualsTest() {
+                var actual = Dnf.builder("Actual").parameter(q).clause(
+                                Dnf.builder("Actual2").parameters(p).clause(friendView.call(p, q)).build().call(q)
+                ).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
+                                List.of(
+                                                List.of(
+                                                                Dnf.builder("Expected2")
+                                                                                .parameters(p)
+                                                                                .clause(friendView.call(p, p))
+                                                                                .build()
+                                                                                .call(q)
+                                                )
+                                )
+                );
+                var error = assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+                assertThat(error.getMessage(), allOf(containsString("Expected2"), containsString("Actual2")));
+        }
+
+        @Test
+        void parameterListLengthMismatchTest() {
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(new SymbolicParameter(p, ParameterDirection.OUT)),
+                                List.of(List.of(friendView.call(p, p)))
+                );
+
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void parameterDirectionMismatchTest() {
+                var actual = Dnf.builder("Actual").parameter(p, ParameterDirection.IN).clause(
+                                personView.call(p)
+                ).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(new SymbolicParameter(p, ParameterDirection.OUT)),
+                                List.of(List.of(personView.call(p)))
+                );
+
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void clauseCountMismatchTest() {
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(p, ParameterDirection.OUT),
+                                                new SymbolicParameter(q, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(friendView.call(p, q)),
+                                                List.of(friendView.call(q, p))
+                                )
+                );
+
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void literalCountMismatchTest() {
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(
+                                List.of(
+                                                new SymbolicParameter(p, ParameterDirection.OUT),
+                                                new SymbolicParameter(q, ParameterDirection.OUT)
+                                ),
+                                List.of(
+                                                List.of(friendView.call(p, q), friendView.call(q, p))
+                                )
+                );
+
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java
new file mode 100644
index 00000000..f716b805
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java
@@ -0,0 +1,127 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.ParameterDirection;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.view.AnySymbolView;
+import tools.refinery.store.query.view.KeyOnlyView;
+import tools.refinery.store.representation.Symbol;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
+
+class StructurallyEqualToTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+        private static final AnySymbolView personView = new KeyOnlyView<>(person);
+        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
+        private static final NodeVariable p = Variable.of("p");
+        private static final NodeVariable q = Variable.of("q");
+
+        @Test
+        void flatEqualsTest() {
+                var expected = Dnf.builder("Expected").parameters(q).clause(personView.call(q)).build();
+                var actual = Dnf.builder("Actual").parameters(p).clause(personView.call(p)).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void flatNotEqualsTest() {
+                var expected = Dnf.builder("Expected").parameters(q).clause(friendView.call(q, q)).build();
+                var actual = Dnf.builder("Actual").parameters(p).clause(friendView.call(p, q)).build();
+
+                var assertion = structurallyEqualTo(expected);
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void deepEqualsTest() {
+                var expected = Dnf.builder("Expected").parameters(q).clause(
+                                Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build().call(q)
+                ).build();
+                var actual = Dnf.builder("Actual").parameters(q).clause(
+                                Dnf.builder("Actual2").parameters(p).clause(personView.call(p)).build().call(q)
+                ).build();
+
+                assertThat(actual, structurallyEqualTo(expected));
+        }
+
+        @Test
+        void deepNotEqualsTest() {
+                var expected = Dnf.builder("Expected").parameters(q).clause(
+                                Dnf.builder("Expected2").parameters(p).clause(friendView.call(p, p)).build().call(q)
+                ).build();
+                var actual = Dnf.builder("Actual").parameter(q).clause(
+                                Dnf.builder("Actual2").parameters(p).clause(friendView.call(p, q)).build().call(q)
+                ).build();
+
+                var assertion = structurallyEqualTo(expected);
+                var error = assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+                assertThat(error.getMessage(), containsString(" called from Expected/1 "));
+        }
+
+        @Test
+        void parameterListLengthMismatchTest() {
+                var expected = Dnf.builder("Expected").parameter(p).clause(
+                                friendView.call(p, p)
+                ).build();
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(expected);
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void parameterDirectionMismatchTest() {
+                var expected = Dnf.builder("Expected").parameter(p, ParameterDirection.OUT).clause(
+                                personView.call(p)
+                ).build();
+                var actual = Dnf.builder("Actual").parameter(p, ParameterDirection.IN).clause(
+                                personView.call(p)
+                ).build();
+
+                var assertion = structurallyEqualTo(expected);
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void clauseCountMismatchTest() {
+                var expected = Dnf.builder("Expected")
+                                .parameters(p, q)
+                                .clause(friendView.call(p, q))
+                                .clause(friendView.call(q, p))
+                                .build();
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(expected);
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+
+        @Test
+        void literalCountMismatchTest() {
+                var expected = Dnf.builder("Expected").parameters(p, q).clause(
+                                friendView.call(p, q),
+                                friendView.call(q, p)
+                ).build();
+                var actual = Dnf.builder("Actual").parameters(p, q).clause(
+                                friendView.call(p, q)
+                ).build();
+
+                var assertion = structurallyEqualTo(expected);
+                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
+        }
+}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/utils/OrderStatisticTreeTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/utils/OrderStatisticTreeTest.java
new file mode 100644
index 00000000..cbb48603
--- /dev/null
+++ b/subprojects/store-query/src/test/java/tools/refinery/store/query/utils/OrderStatisticTreeTest.java
@@ -0,0 +1,634 @@
+/*
+ * Copyright (c) 2021 Rodion Efremov
+ * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: MIT OR EPL-2.0
+ */
+package tools.refinery.store.query.utils;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.util.*;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+/**
+ * Tests for an order statistic tree which is based on AVL-trees.
+ * <p>
+ * This class was copied into <i>Refinery</i> from
+ * <a href="https://github.com/coderodde/OrderStatisticTree/tree/546c343b9f5d868e394a079ff32691c9dbfd83e3">https://github.com/coderodde/OrderStatisticTree</a>
+ * and is available under the
+ * <a href="https://github.com/coderodde/OrderStatisticTree/blob/master/LICENSE">MIT License</a>.
+ * We also migrated the code to Junit 5, cleaned up some linter warnings, and made the tests deterministic by fixing
+ * the random seeds.
+ *
+ * @author Rodion "rodde" Efremov
+ * @version based on 1.6 (Feb 11, 2016)
+ */
+class OrderStatisticTreeTest {
+        private final OrderStatisticTree<Integer> tree = new OrderStatisticTree<>();
+
+        private final TreeSet<Integer> set = new TreeSet<>();
+
+        @BeforeEach
+        void before() {
+                tree.clear();
+                set.clear();
+        }
+
+        @Test
+        void testAdd() {
+                assertEquals(set.isEmpty(), tree.isEmpty());
+
+                for (int i = 10; i < 30; i += 2) {
+                        assertTrue(tree.isHealthy());
+                        assertEquals(set.contains(i), tree.contains(i));
+                        assertEquals(set.add(i), tree.add(i));
+                        assertEquals(set.add(i), tree.add(i));
+                        assertEquals(set.contains(i), tree.contains(i));
+                        assertTrue(tree.isHealthy());
+                }
+
+                assertEquals(set.isEmpty(), tree.isEmpty());
+        }
+
+        @Test
+        void testAddAll() {
+                for (int i = 0; i < 10; ++i) {
+                        assertEquals(set.add(i), tree.add(i));
+                }
+
+                Collection<Integer> coll = Arrays.asList(10, 9, 7, 11, 12);
+
+                assertEquals(set.addAll(coll), tree.addAll(coll));
+                assertEquals(set.size(), tree.size());
+
+                for (int i = -10; i < 20; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+        }
+
+        @Test
+        void testClear() {
+                for (int i = 0; i < 2000; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                assertEquals(set.size(), tree.size());
+                set.clear();
+                tree.clear();
+                // We expect {@code tree.size()} to always be 0, but we also test for it.
+                //noinspection ConstantValue
+                assertEquals(0, tree.size());
+        }
+
+        @Test
+        void testContains() {
+                for (int i = 100; i < 200; i += 3) {
+                        assertTrue(tree.isHealthy());
+                        assertEquals(set.add(i), tree.add(i));
+                        assertTrue(tree.isHealthy());
+                }
+
+                assertEquals(set.size(), tree.size());
+
+                for (int i = 0; i < 300; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+        }
+
+        @Test
+        void testContainsAll() {
+                for (int i = 0; i < 50; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Collection<Integer> coll = new HashSet<>();
+
+                for (int i = 10; i < 20; ++i) {
+                        coll.add(i);
+                }
+
+                assertEquals(set.containsAll(coll), tree.containsAll(coll));
+                coll.add(100);
+                assertEquals(set.containsAll(coll), tree.containsAll(coll));
+        }
+
+        @Test
+        void testRemove() {
+                for (int i = 0; i < 200; ++i) {
+                        assertEquals(set.add(i), tree.add(i));
+                }
+
+                for (int i = 50; i < 150; i += 2) {
+                        assertEquals(set.remove(i), tree.remove(i));
+                        assertTrue(tree.isHealthy());
+                }
+
+                for (int i = -100; i < 300; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+        }
+
+        @Test
+        void testRemoveLast() {
+                tree.add(1);
+                tree.remove(1);
+                assertEquals(0, tree.size());
+        }
+
+        @Test
+        void testRemoveAll() {
+                for (int i = 0; i < 40; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Collection<Integer> coll = new HashSet<>();
+
+                for (int i = 10; i < 20; ++i) {
+                        coll.add(i);
+                }
+
+                assertEquals(set.removeAll(coll), tree.removeAll(coll));
+
+                for (int i = -10; i < 50; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+
+                assertEquals(set.removeAll(coll), tree.removeAll(coll));
+
+                for (int i = -10; i < 50; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+        }
+
+        @Test
+        void testSize() {
+                for (int i = 0; i < 200; ++i) {
+                        assertEquals(set.size(), tree.size());
+                        assertEquals(set.add(i), tree.add(i));
+                        assertEquals(set.size(), tree.size());
+                }
+        }
+
+        @Test
+        void testIndexOf() {
+                for (int i = 0; i < 100; ++i) {
+                        assertTrue(tree.add(i * 2));
+                }
+
+                for (int i = 0; i < 100; ++i) {
+                        assertEquals(i, tree.indexOf(2 * i));
+                }
+
+                for (int i = 100; i < 150; ++i) {
+                        assertEquals(-1, tree.indexOf(2 * i));
+                }
+        }
+
+        @Test
+        void testEmpty() {
+                assertEquals(set.isEmpty(), tree.isEmpty());
+                set.add(0);
+                tree.add(0);
+                assertEquals(set.isEmpty(), tree.isEmpty());
+        }
+
+        @Test
+        void testEmptyTreeGetThrowsOnNegativeIndex() {
+                assertThrows(IndexOutOfBoundsException.class, () -> tree.get(-1));
+        }
+
+        @Test
+        void testEmptyTreeSelectThrowsOnTooLargeIndex() {
+                assertThrows(IndexOutOfBoundsException.class, () -> tree.get(0));
+        }
+
+        @Test
+        void testSelectThrowsOnNegativeIndex() {
+                for (int i = 0; i < 5; ++i) {
+                        tree.add(i);
+                }
+
+                assertThrows(IndexOutOfBoundsException.class, () -> tree.get(-1));
+        }
+
+        @Test
+        void testSelectThrowsOnTooLargeIndex() {
+                for (int i = 0; i < 5; ++i) {
+                        tree.add(i);
+                }
+
+                assertThrows(IndexOutOfBoundsException.class, () -> tree.get(5));
+        }
+
+        @Test
+        void testGet() {
+                for (int i = 0; i < 100; i += 3) {
+                        tree.add(i);
+                }
+
+                for (int i = 0; i < tree.size(); ++i) {
+                        assertEquals(Integer.valueOf(3 * i), tree.get(i));
+                }
+        }
+
+        @Test
+        void findBug() {
+                tree.add(0);
+                assertTrue(tree.isHealthy());
+
+                tree.add(-1);
+                tree.remove(-1);
+                assertTrue(tree.isHealthy());
+
+                tree.add(1);
+                tree.remove(1);
+                assertTrue(tree.isHealthy());
+
+                tree.add(-1);
+                tree.add(1);
+                tree.remove(0);
+                assertTrue(tree.isHealthy());
+
+                tree.clear();
+                tree.add(0);
+                tree.add(-1);
+                tree.add(10);
+                tree.add(5);
+                tree.add(15);
+                tree.add(11);
+                tree.add(30);
+                tree.add(7);
+
+                tree.remove(-1);
+
+                assertTrue(tree.isHealthy());
+        }
+
+        @ParameterizedTest(name = "seed = {0}")
+        @MethodSource("seedSource")
+        void tryReproduceTheCounterBug(long seed) {
+                Random random = new Random(seed);
+                List<Integer> list = new ArrayList<>();
+
+                for (int i = 0; i < 10; ++i) {
+                        int number = random.nextInt(1000);
+                        list.add(number);
+                        tree.add(number);
+                        assertTrue(tree.isHealthy());
+                }
+
+                for (Integer i : list) {
+                        tree.remove(i);
+                        boolean healthy = tree.isHealthy();
+                        assertTrue(healthy);
+                }
+        }
+
+        @Test
+        void testEmptyIterator() {
+                var iterator = tree.iterator();
+                assertThrows(NoSuchElementException.class, iterator::next);
+        }
+
+        @Test
+        void testIteratorThrowsOnDoubleRemove() {
+                for (int i = 10; i < 20; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                for (int i = 0; i < 3; ++i) {
+                        assertEquals(iterator1.next(), iterator2.next());
+                }
+
+                iterator1.remove();
+                iterator2.remove();
+
+                assertThrows(IllegalStateException.class, iterator1::remove);
+                assertThrows(IllegalStateException.class, iterator2::remove);
+        }
+
+        @Test
+        void testIterator() {
+                for (int i = 0; i < 5; ++i) {
+                        tree.add(i);
+                        set.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                for (int i = 0; i < 5; ++i) {
+                        assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                        assertEquals(iterator1.next(), iterator2.next());
+                }
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+
+                assertThrows(NoSuchElementException.class, iterator1::next);
+                assertThrows(NoSuchElementException.class, iterator2::next);
+        }
+
+        @Test
+        void testRemoveBeforeNextThrowsEmpty() {
+                var setIterator = set.iterator();
+                assertThrows(IllegalStateException.class, setIterator::remove);
+
+                var treeIterator = tree.iterator();
+                assertThrows(IllegalStateException.class, treeIterator::remove);
+        }
+
+        @Test
+        void testRemoveThrowsWithoutNext() {
+                for (int i = 0; i < 10; ++i) {
+                        tree.add(i);
+                        set.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                for (int i = 0; i < 4; ++i) {
+                        assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                        assertEquals(iterator1.next(), iterator2.next());
+                }
+
+                iterator1.remove();
+                iterator2.remove();
+
+                assertThrows(IllegalStateException.class, iterator1::remove);
+                assertThrows(IllegalStateException.class, iterator2::remove);
+        }
+
+        @Test
+        void testRetainAll() {
+                for (int i = 0; i < 100; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Collection<Integer> coll = Arrays.asList(26, 29, 25);
+
+                assertEquals(set.retainAll(coll), tree.retainAll(coll));
+                assertEquals(set.size(), tree.size());
+
+                assertTrue(set.containsAll(tree));
+                assertTrue(tree.containsAll(set));
+        }
+
+        @Test
+        void testIteratorRemove() {
+                for (int i = 10; i < 16; ++i) {
+                        assertEquals(set.add(i), tree.add(i));
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                assertEquals(iterator1.next(), iterator2.next());
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                assertEquals(iterator1.next(), iterator2.next());
+
+                iterator1.remove(); // remove 11
+                iterator2.remove();
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                assertEquals(iterator1.next(), iterator2.next());
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+                assertEquals(iterator1.next(), iterator2.next());
+
+                iterator1.remove(); // remove 13
+                iterator2.remove();
+
+                assertEquals(set.size(), tree.size());
+
+                for (int i = 10; i < 16; ++i) {
+                        assertEquals(set.contains(i), tree.contains(i));
+                }
+        }
+
+        @ParameterizedTest(name = "seed = {0}")
+        @MethodSource("seedSource")
+        void testIteratorBruteForce(long seed) {
+                for (int i = 0; i < 1000; ++i) {
+                        assertEquals(set.add(i), tree.add(i));
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                Random random = new Random(seed);
+
+                while (true) {
+                        if (!iterator1.hasNext()) {
+                                assertFalse(iterator2.hasNext());
+                                break;
+                        }
+
+                        boolean toRemove = random.nextBoolean();
+
+                        if (toRemove) {
+                                boolean thrown = false;
+
+                                try {
+                                        iterator1.remove();
+                                } catch (IllegalStateException ex) {
+                                        thrown = true;
+                                }
+
+                                if (thrown) {
+                                        assertThrows(IllegalStateException.class, iterator2::remove);
+                                } else {
+                                        iterator2.remove();
+                                }
+                        } else {
+                                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+
+                                if (iterator1.hasNext()) {
+                                        assertEquals(iterator1.next(), iterator2.next());
+                                } else {
+                                        break;
+                                }
+                        }
+                }
+
+                assertEquals(set.size(), tree.size());
+                assertTrue(tree.isHealthy());
+                assertTrue(set.containsAll(tree));
+                assertTrue(tree.containsAll(set));
+        }
+
+        @Test
+        void testIteratorConcurrentModification() {
+                for (int i = 0; i < 100; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                set.remove(10);
+                tree.remove(10);
+
+                assertEquals(iterator1.hasNext(), iterator2.hasNext());
+
+                boolean thrown = false;
+
+                try {
+                        iterator1.next();
+                } catch (ConcurrentModificationException ex) {
+                        thrown = true;
+                }
+
+                if (thrown) {
+                        assertThrows(ConcurrentModificationException.class, iterator2::next);
+                } else {
+                        iterator2.next();
+                }
+        }
+
+        @Test
+        void testIteratorConcurrentRemove() {
+                for (int i = 10; i < 20; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                for (int i = 0; i < 4; ++i) {
+                        iterator1.next();
+                        iterator2.next();
+                }
+
+                // None of them contains 2, should not change the modification count.
+                set.remove(2);
+                tree.remove(2);
+
+                iterator1.remove();
+                iterator2.remove();
+
+                iterator1.next();
+                iterator2.next();
+
+                set.remove(12);
+                tree.remove(12);
+
+                // Both of them should throw.
+                assertThrows(ConcurrentModificationException.class, iterator1::remove);
+                assertThrows(ConcurrentModificationException.class, iterator2::remove);
+        }
+
+        @Test
+        void testConcurrentOrIllegalStateOnRemove() {
+                for (int i = 0; i < 10; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Iterator<Integer> iterator1 = set.iterator();
+                Iterator<Integer> iterator2 = tree.iterator();
+
+                set.add(100);
+                tree.add(100);
+
+                assertThrows(IllegalStateException.class, iterator1::remove);
+                assertThrows(IllegalStateException.class, iterator2::remove);
+        }
+
+        @Test
+        void testConcurrentIterators() {
+                for (int i = 0; i < 10; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Iterator<Integer> iterator1a = set.iterator();
+                Iterator<Integer> iterator1b = set.iterator();
+                Iterator<Integer> iterator2a = tree.iterator();
+                Iterator<Integer> iterator2b = tree.iterator();
+
+                for (int i = 0; i < 3; ++i) {
+                        iterator1a.next();
+                        iterator2a.next();
+                }
+
+                iterator1a.remove();
+                iterator2a.remove();
+
+                assertEquals(iterator1b.hasNext(), iterator2b.hasNext());
+
+                assertThrows(ConcurrentModificationException.class, iterator1b::next);
+                assertThrows(ConcurrentModificationException.class, iterator2b::next);
+        }
+
+        @ParameterizedTest(name = "seed = {0}")
+        @MethodSource("seedSource")
+        void testToArray(long seed) {
+                Random r = new Random(seed);
+
+                for (int i = 0; i < 50; ++i) {
+                        int num = r.nextInt();
+                        set.add(num);
+                        tree.add(num);
+                }
+
+                assertArrayEquals(set.toArray(), tree.toArray());
+        }
+
+        @Test
+        void testToArrayGeneric() {
+                for (int i = 0; i < 100; ++i) {
+                        set.add(i);
+                        tree.add(i);
+                }
+
+                Integer[] array1before = new Integer[99];
+                Integer[] array2before = new Integer[99];
+
+                Integer[] array1after = set.toArray(array1before);
+                Integer[] array2after = tree.toArray(array2before);
+
+                assertNotSame(array1before, array1after);
+                assertNotSame(array2before, array2after);
+                assertArrayEquals(array1after, array2after);
+
+                set.remove(1);
+                tree.remove(1);
+
+                array1after = set.toArray(array1before);
+                array2after = tree.toArray(array2before);
+
+                assertSame(array1before, array1after);
+                assertSame(array2before, array2after);
+                assertArrayEquals(array1after, array2after);
+        }
+
+        static Stream<Arguments> seedSource() {
+                return Stream.of(
+                                Arguments.of(0L),
+                                Arguments.of(1L),
+                                Arguments.of(2L),
+                                Arguments.of(3L),
+                                Arguments.of(4L)
+                );
+        }
+}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java
new file mode 100644
index 00000000..6a3301b3
--- /dev/null
+++ b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java
@@ -0,0 +1,68 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.hamcrest.Description;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.List;
+
+class MismatchDescribingDnfEqualityChecker extends DeepDnfEqualityChecker {
+        private final Description description;
+        private boolean raw;
+        private boolean needsDescription = true;
+
+        MismatchDescribingDnfEqualityChecker(Description description) {
+                this.description = description;
+        }
+
+        public boolean needsDescription() {
+                return needsDescription;
+        }
+
+        @Override
+        public boolean dnfEqualRaw(List<SymbolicParameter> symbolicParameters, List<? extends List<? extends Literal>> clauses, Dnf other) {
+                try {
+                        raw = true;
+                        boolean result = super.dnfEqualRaw(symbolicParameters, clauses, other);
+                        if (!result && needsDescription) {
+                                description.appendText("was ").appendText(other.toDefinitionString());
+                        }
+                        return false;
+                } finally {
+                        raw = false;
+                }
+        }
+
+        @Override
+        protected boolean doCheckEqual(Pair pair) {
+                boolean result = super.doCheckEqual(pair);
+                if (!result && needsDescription) {
+                        describeMismatch(pair);
+                        // Only describe the first found (innermost) mismatch.
+                        needsDescription = false;
+                }
+                return result;
+        }
+
+        private void describeMismatch(Pair pair) {
+                var inProgress = getInProgress();
+                int size = inProgress.size();
+                if (size <= 1 && !raw) {
+                        description.appendText("was ").appendText(pair.right().toDefinitionString());
+                        return;
+                }
+                var last = inProgress.get(size - 1);
+                description.appendText("expected ").appendText(last.left().toDefinitionString());
+                for (int i = size - 2; i >= 0; i--) {
+                        description.appendText(" called from ").appendText(inProgress.get(i).left().toString());
+                }
+                description.appendText(" was not structurally equal to ").appendText(last.right().toDefinitionString());
+        }
+}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java
new file mode 100644
index 00000000..cd449a6a
--- /dev/null
+++ b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java
@@ -0,0 +1,46 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.hamcrest.Matcher;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.List;
+
+public final class QueryMatchers {
+        private QueryMatchers() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        /**
+         * Compare two {@link Dnf} instances up to renaming of variables.
+         *
+         * @param expected The expected {@link Dnf} instance.
+         * @return A Hamcrest matcher for equality up to renaming of variables.
+         */
+        public static Matcher<Dnf> structurallyEqualTo(Dnf expected) {
+                return new StructurallyEqualTo(expected);
+        }
+
+        /**
+         * Compare a {@link Dnf} instance to another predicate in DNF form without constructing it.
+         * <p>
+         * This matcher should be used instead of {@link #structurallyEqualTo(Dnf)} when the validation and
+         * pre-processing associated with the {@link Dnf} constructor, i.e., validation of parameter directions,
+         * topological sorting of literals, and the reduction of trivial predicates is not desired. In particular, this
+         * matcher can be used to test for exact order of literal after pre-processing.
+         *
+         * @param expectedSymbolicParameters The expected list of symbolic parameters.
+         * @param expectedLiterals The expected clauses. Each clause is represented by a list of literals.
+         * @return A Hamcrest matcher for equality up to renaming of variables.
+         */
+        public static Matcher<Dnf> structurallyEqualTo(List<SymbolicParameter> expectedSymbolicParameters,
+                                                                                                   List<? extends List<? extends Literal>> expectedLiterals) {
+                return new StructurallyEqualToRaw(expectedSymbolicParameters, expectedLiterals);
+        }
+}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java
new file mode 100644
index 00000000..86149141
--- /dev/null
+++ b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java
@@ -0,0 +1,41 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.hamcrest.Description;
+import org.hamcrest.TypeSafeMatcher;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
+
+public class StructurallyEqualTo extends TypeSafeMatcher<Dnf> {
+        private final Dnf expected;
+
+        public StructurallyEqualTo(Dnf expected) {
+                this.expected = expected;
+        }
+
+        @Override
+        protected boolean matchesSafely(Dnf item) {
+                var checker = new DeepDnfEqualityChecker();
+                return checker.dnfEqual(expected, item);
+        }
+
+        @Override
+        protected void describeMismatchSafely(Dnf item, Description mismatchDescription) {
+                var describingChecker = new MismatchDescribingDnfEqualityChecker(mismatchDescription);
+                if (describingChecker.dnfEqual(expected, item)) {
+                        throw new IllegalStateException("Mismatched Dnf was matching on repeated comparison");
+                }
+                if (describingChecker.needsDescription()) {
+                        super.describeMismatchSafely(item, mismatchDescription);
+                }
+        }
+
+        @Override
+        public void describeTo(Description description) {
+                description.appendText("structurally equal to ").appendText(expected.toDefinitionString());
+        }
+}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java
new file mode 100644
index 00000000..2f8c2944
--- /dev/null
+++ b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java
@@ -0,0 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.query.tests;
+
+import org.hamcrest.Description;
+import org.hamcrest.TypeSafeMatcher;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.List;
+
+public class StructurallyEqualToRaw extends TypeSafeMatcher<Dnf> {
+        private final List<SymbolicParameter> expectedSymbolicParameters;
+        private final List<? extends List<? extends Literal>> expectedClauses;
+
+        public StructurallyEqualToRaw(List<SymbolicParameter> expectedSymbolicParameters,
+                                                                  List<? extends List<? extends Literal>> expectedClauses) {
+                this.expectedSymbolicParameters = expectedSymbolicParameters;
+                this.expectedClauses = expectedClauses;
+        }
+
+        @Override
+        protected boolean matchesSafely(Dnf item) {
+                var checker = new DeepDnfEqualityChecker();
+                return checker.dnfEqualRaw(expectedSymbolicParameters, expectedClauses, item);
+        }
+
+        @Override
+        protected void describeMismatchSafely(Dnf item, Description mismatchDescription) {
+                var describingChecker = new MismatchDescribingDnfEqualityChecker(mismatchDescription);
+                if (describingChecker.dnfEqualRaw(expectedSymbolicParameters, expectedClauses, item)) {
+                        throw new IllegalStateException("Mismatched Dnf was matching on repeated comparison");
+                }
+                if (describingChecker.needsDescription()) {
+                        super.describeMismatchSafely(item, mismatchDescription);
+                }
+        }
+
+        @Override
+        public void describeTo(Description description) {
+                description.appendText("structurally equal to ")
+                                .appendValueList("(", ", ", ")", expectedSymbolicParameters)
+                                .appendText(" <-> ")
+                                .appendValueList("", ", ", ".", expectedClauses);
+        }
+}
diff --git a/subprojects/store-reasoning/build.gradle.kts b/subprojects/store-reasoning/build.gradle.kts
new file mode 100644
index 00000000..abad0491
--- /dev/null
+++ b/subprojects/store-reasoning/build.gradle.kts
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+}
+
+dependencies {
+        api(project(":refinery-store-query"))
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/AnyPartialInterpretation.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/AnyPartialInterpretation.java
new file mode 100644
index 00000000..000171a1
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/AnyPartialInterpretation.java
@@ -0,0 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+
+public sealed interface AnyPartialInterpretation permits PartialInterpretation {
+        ReasoningAdapter getAdapter();
+
+        AnyPartialSymbol getPartialSymbol();
+
+        int countUnfinished();
+
+        int countErrors();
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/MergeResult.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/MergeResult.java
new file mode 100644
index 00000000..d3a216d8
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/MergeResult.java
@@ -0,0 +1,20 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+public enum MergeResult {
+        UNCHANGED,
+        REFINED,
+        REJECTED;
+
+        public MergeResult andAlso(MergeResult other) {
+                return switch (this) {
+                        case UNCHANGED -> other;
+                        case REFINED -> other == REJECTED ? REJECTED : REFINED;
+                        case REJECTED -> REJECTED;
+                };
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/PartialInterpretation.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/PartialInterpretation.java
new file mode 100644
index 00000000..4140d640
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/PartialInterpretation.java
@@ -0,0 +1,25 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+import tools.refinery.store.reasoning.representation.PartialSymbol;
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+public non-sealed interface PartialInterpretation<A, C> extends AnyPartialInterpretation {
+        @Override
+        PartialSymbol<A, C> getPartialSymbol();
+
+        A get(Tuple key);
+
+        Cursor<Tuple, A> getAll();
+
+        MergeResult merge(Tuple key, A value);
+
+        C getConcrete(Tuple key);
+
+        Cursor<Tuple, C> getAllConcrete();
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java
new file mode 100644
index 00000000..6d5d6f89
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.query.resultset.ResultSet;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.reasoning.representation.PartialSymbol;
+
+public interface ReasoningAdapter extends ModelAdapter {
+        PartialRelation EXISTS = new PartialRelation("exists", 1);
+
+        @Override
+        ReasoningStoreAdapter getStoreAdapter();
+
+        default AnyPartialInterpretation getPartialInterpretation(AnyPartialSymbol partialSymbol) {
+                // Cast to disambiguate overloads.
+                var typedPartialSymbol = (PartialSymbol<?, ?>) partialSymbol;
+                return getPartialInterpretation(typedPartialSymbol);
+        }
+
+        <A, C> PartialInterpretation<A, C> getPartialInterpretation(PartialSymbol<A, C> partialSymbol);
+
+        ResultSet<Boolean> getLiftedResultSet(Dnf query);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java
new file mode 100644
index 00000000..d3a337e8
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java
@@ -0,0 +1,33 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.reasoning.literal.Modality;
+import tools.refinery.store.query.dnf.Dnf;
+
+import java.util.Collection;
+import java.util.List;
+
+@SuppressWarnings("UnusedReturnValue")
+public interface ReasoningBuilder extends ModelAdapterBuilder {
+        default ReasoningBuilder liftedQueries(Dnf... liftedQueries) {
+                return liftedQueries(List.of(liftedQueries));
+        }
+
+        default ReasoningBuilder liftedQueries(Collection<Dnf> liftedQueries) {
+                liftedQueries.forEach(this::liftedQuery);
+                return this;
+        }
+
+        ReasoningBuilder liftedQuery(Dnf liftedQuery);
+
+        Dnf lift(Modality modality, Dnf query);
+
+        @Override
+        ReasoningStoreAdapter build(ModelStore store);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningStoreAdapter.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningStoreAdapter.java
new file mode 100644
index 00000000..c9795255
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningStoreAdapter.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning;
+
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+import tools.refinery.store.query.dnf.Dnf;
+
+import java.util.Collection;
+
+public interface ReasoningStoreAdapter extends ModelStoreAdapter {
+        Collection<AnyPartialSymbol> getPartialSymbols();
+
+        Collection<Dnf> getLiftedQueries();
+
+        @Override
+        ReasoningAdapter createModelAdapter(Model model);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java
new file mode 100644
index 00000000..1bd3ad2e
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.internal;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.reasoning.ReasoningAdapter;
+import tools.refinery.store.reasoning.PartialInterpretation;
+import tools.refinery.store.reasoning.representation.PartialSymbol;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.resultset.ResultSet;
+
+public class ReasoningAdapterImpl implements ReasoningAdapter {
+        private final Model model;
+        private final ReasoningStoreAdapterImpl storeAdapter;
+
+        ReasoningAdapterImpl(Model model, ReasoningStoreAdapterImpl storeAdapter) {
+                this.model = model;
+                this.storeAdapter = storeAdapter;
+        }
+
+        @Override
+        public Model getModel() {
+                return model;
+        }
+
+        @Override
+        public ReasoningStoreAdapterImpl getStoreAdapter() {
+                return storeAdapter;
+        }
+
+        @Override
+        public <A, C> PartialInterpretation<A, C> getPartialInterpretation(PartialSymbol<A, C> partialSymbol) {
+                return null;
+        }
+
+        @Override
+        public ResultSet<Boolean> getLiftedResultSet(Dnf query) {
+                return null;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java
new file mode 100644
index 00000000..aa71496c
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java
@@ -0,0 +1,31 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.internal;
+
+import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.reasoning.ReasoningBuilder;
+import tools.refinery.store.reasoning.literal.Modality;
+
+public class ReasoningBuilderImpl extends AbstractModelAdapterBuilder<ReasoningStoreAdapterImpl>
+                implements ReasoningBuilder {
+        @Override
+        public ReasoningBuilder liftedQuery(Dnf liftedQuery) {
+                return null;
+        }
+
+        @Override
+        public Dnf lift(Modality modality, Dnf query) {
+                checkNotConfigured();
+                return null;
+        }
+
+        @Override
+        public ReasoningStoreAdapterImpl doBuild(ModelStore store) {
+                return null;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningStoreAdapterImpl.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningStoreAdapterImpl.java
new file mode 100644
index 00000000..cdddd8d6
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningStoreAdapterImpl.java
@@ -0,0 +1,42 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.internal;
+
+import tools.refinery.store.reasoning.ReasoningStoreAdapter;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+import tools.refinery.store.query.dnf.Dnf;
+
+import java.util.Collection;
+
+public class ReasoningStoreAdapterImpl implements ReasoningStoreAdapter {
+        private final ModelStore store;
+
+        ReasoningStoreAdapterImpl(ModelStore store) {
+                this.store = store;
+        }
+
+        @Override
+        public ModelStore getStore() {
+                return store;
+        }
+
+        @Override
+        public Collection<AnyPartialSymbol> getPartialSymbols() {
+                return null;
+        }
+
+        @Override
+        public Collection<Dnf> getLiftedQueries() {
+                return null;
+        }
+
+        @Override
+        public ReasoningAdapterImpl createModelAdapter(Model model) {
+                return new ReasoningAdapterImpl(model, this);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java
new file mode 100644
index 00000000..ac41d170
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java
@@ -0,0 +1,128 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.lifting;
+
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.dnf.DnfBuilder;
+import tools.refinery.store.query.dnf.DnfClause;
+import tools.refinery.store.query.literal.CallLiteral;
+import tools.refinery.store.query.literal.CallPolarity;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.reasoning.ReasoningAdapter;
+import tools.refinery.store.reasoning.literal.ModalConstraint;
+import tools.refinery.store.reasoning.literal.Modality;
+import tools.refinery.store.reasoning.literal.PartialLiterals;
+import tools.refinery.store.util.CycleDetectingMapper;
+
+import java.util.ArrayList;
+import java.util.LinkedHashSet;
+import java.util.List;
+
+public class DnfLifter {
+        private final CycleDetectingMapper<ModalDnf, Dnf> mapper = new CycleDetectingMapper<>(ModalDnf::toString,
+                        this::doLift);
+
+        public Dnf lift(Modality modality, Dnf query) {
+                return mapper.map(new ModalDnf(modality, query));
+        }
+
+        private Dnf doLift(ModalDnf modalDnf) {
+                var modality = modalDnf.modality();
+                var dnf = modalDnf.dnf();
+                var builder = Dnf.builder();
+                builder.symbolicParameters(dnf.getSymbolicParameters());
+                boolean changed = false;
+                for (var clause : dnf.getClauses()) {
+                        if (liftClause(modality, dnf, clause, builder)) {
+                                changed = true;
+                        }
+                }
+                if (changed) {
+                        return builder.build();
+                }
+                return dnf;
+        }
+
+        private boolean liftClause(Modality modality, Dnf originalDnf, DnfClause clause, DnfBuilder builder) {
+                boolean changed = false;
+                var quantifiedVariables = getQuantifiedDataVariables(originalDnf, clause);
+                var literals = clause.literals();
+                var liftedLiterals = new ArrayList<Literal>(literals.size());
+                for (var literal : literals) {
+                        Literal liftedLiteral = liftLiteral(modality, literal);
+                        if (liftedLiteral == null) {
+                                liftedLiteral = literal;
+                        } else {
+                                changed = true;
+                        }
+                        liftedLiterals.add(liftedLiteral);
+                        var variable = isExistsLiteralForVariable(modality, liftedLiteral);
+                        if (variable != null) {
+                                // If we already quantify over the existence of the variable with the expected modality,
+                                // we don't need to insert quantification manually.
+                                quantifiedVariables.remove(variable);
+                        }
+                }
+                for (var quantifiedVariable : quantifiedVariables) {
+                        // Quantify over data variables that are not already quantified with the expected modality.
+                        liftedLiterals.add(new CallLiteral(CallPolarity.POSITIVE,
+                                        new ModalConstraint(modality, ReasoningAdapter.EXISTS), List.of(quantifiedVariable)));
+                }
+                builder.clause(liftedLiterals);
+                return changed || !quantifiedVariables.isEmpty();
+        }
+
+        private static LinkedHashSet<Variable> getQuantifiedDataVariables(Dnf originalDnf, DnfClause clause) {
+                var quantifiedVariables = new LinkedHashSet<>(clause.positiveVariables());
+                for (var symbolicParameter : originalDnf.getSymbolicParameters()) {
+                        // The existence of parameters will be checked outside this DNF.
+                        quantifiedVariables.remove(symbolicParameter.getVariable());
+                }
+                quantifiedVariables.removeIf(variable -> !(variable instanceof NodeVariable));
+                return quantifiedVariables;
+        }
+
+        @Nullable
+        private Variable isExistsLiteralForVariable(Modality modality, Literal literal) {
+                if (literal instanceof CallLiteral callLiteral &&
+                                callLiteral.getPolarity() == CallPolarity.POSITIVE &&
+                                callLiteral.getTarget() instanceof ModalConstraint modalConstraint &&
+                                modalConstraint.modality() == modality &&
+                                modalConstraint.constraint().equals(ReasoningAdapter.EXISTS)) {
+                        return callLiteral.getArguments().get(0);
+                }
+                return null;
+        }
+
+        @Nullable
+        private Literal liftLiteral(Modality modality, Literal literal) {
+                if (!(literal instanceof CallLiteral callLiteral)) {
+                        return null;
+                }
+                var target = callLiteral.getTarget();
+                if (target instanceof ModalConstraint modalTarget) {
+                        var actualTarget = modalTarget.constraint();
+                        if (actualTarget instanceof Dnf dnf) {
+                                var targetModality = modalTarget.modality();
+                                var liftedTarget = lift(targetModality, dnf);
+                                return new CallLiteral(callLiteral.getPolarity(), liftedTarget, callLiteral.getArguments());
+                        }
+                        // No more lifting to be done, pass any modal call to a partial symbol through.
+                        return null;
+                } else if (target instanceof Dnf dnf) {
+                        var polarity = callLiteral.getPolarity();
+                        var liftedTarget = lift(modality.commute(polarity), dnf);
+                        // Use == instead of equals(), because lift will return the same object by reference is there are no
+                        // changes made during lifting.
+                        return liftedTarget == target ? null : new CallLiteral(polarity, liftedTarget, callLiteral.getArguments());
+                } else {
+                        return PartialLiterals.addModality(callLiteral, modality);
+                }
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/ModalDnf.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/ModalDnf.java
new file mode 100644
index 00000000..16fb8fbf
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/ModalDnf.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.lifting;
+
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.reasoning.literal.Modality;
+
+record ModalDnf(Modality modality, Dnf dnf) {
+        @Override
+        public String toString() {
+                return "%s %s".formatted(modality, dnf.name());
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/ModalConstraint.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/ModalConstraint.java
new file mode 100644
index 00000000..4e5a6099
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/ModalConstraint.java
@@ -0,0 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.literal;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.equality.LiteralEqualityHelper;
+import tools.refinery.store.query.literal.Reduction;
+import tools.refinery.store.query.term.Parameter;
+
+import java.util.List;
+
+public record ModalConstraint(Modality modality, Constraint constraint) implements Constraint {
+        private static final String FORMAT = "%s %s";
+
+        @Override
+        public String name() {
+                return FORMAT.formatted(modality, constraint.name());
+        }
+
+        @Override
+        public List<Parameter> getParameters() {
+                return constraint.getParameters();
+        }
+
+        @Override
+        public Reduction getReduction() {
+                return constraint.getReduction();
+        }
+
+        @Override
+        public boolean equals(LiteralEqualityHelper helper, Constraint other) {
+                if (getClass() != other.getClass()) {
+                        return false;
+                }
+                var otherModalConstraint = (ModalConstraint) other;
+                return modality == otherModalConstraint.modality && constraint.equals(helper, otherModalConstraint.constraint);
+        }
+
+        @Override
+        public String toReferenceString() {
+                return FORMAT.formatted(modality, constraint.toReferenceString());
+        }
+
+        @Override
+        public String toString() {
+                return FORMAT.formatted(modality, constraint);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/Modality.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/Modality.java
new file mode 100644
index 00000000..96466d5c
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/Modality.java
@@ -0,0 +1,36 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.literal;
+
+import tools.refinery.store.query.literal.CallPolarity;
+
+import java.util.Locale;
+
+public enum Modality {
+        MUST,
+        MAY,
+        CURRENT;
+
+        public Modality negate() {
+                return switch(this) {
+                        case MUST -> MAY;
+                        case MAY -> MUST;
+                        case CURRENT -> CURRENT;
+                };
+        }
+
+        public Modality commute(CallPolarity polarity) {
+                if (polarity.isPositive()) {
+                        return this;
+                }
+                return this.negate();
+        }
+
+        @Override
+        public String toString() {
+                return name().toLowerCase(Locale.ROOT);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/PartialLiterals.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/PartialLiterals.java
new file mode 100644
index 00000000..0e46a795
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/literal/PartialLiterals.java
@@ -0,0 +1,36 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.literal;
+
+import tools.refinery.store.query.literal.CallLiteral;
+
+public final class PartialLiterals {
+        private PartialLiterals() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static CallLiteral may(CallLiteral literal) {
+                return addModality(literal, Modality.MAY);
+        }
+
+        public static CallLiteral must(CallLiteral literal) {
+                return addModality(literal, Modality.MUST);
+        }
+
+        public static CallLiteral current(CallLiteral literal) {
+                return addModality(literal, Modality.CURRENT);
+        }
+
+        public static CallLiteral addModality(CallLiteral literal, Modality modality) {
+                var target = literal.getTarget();
+                if (target instanceof ModalConstraint) {
+                        throw new IllegalArgumentException("Literal %s already has modality".formatted(literal));
+                }
+                var polarity = literal.getPolarity();
+                var modalTarget = new ModalConstraint(modality.commute(polarity), target);
+                return new CallLiteral(polarity, modalTarget, literal.getArguments());
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialFunction.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialFunction.java
new file mode 100644
index 00000000..8d2cb5cf
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialFunction.java
@@ -0,0 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.representation;
+
+public sealed interface AnyPartialFunction extends AnyPartialSymbol permits PartialFunction {
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialSymbol.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialSymbol.java
new file mode 100644
index 00000000..788eef73
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/AnyPartialSymbol.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.representation;
+
+import tools.refinery.store.representation.AnyAbstractDomain;
+
+public sealed interface AnyPartialSymbol permits AnyPartialFunction, PartialSymbol {
+        String name();
+
+        int arity();
+
+        AnyAbstractDomain abstractDomain();
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialFunction.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialFunction.java
new file mode 100644
index 00000000..d58d026f
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialFunction.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.representation;
+
+import tools.refinery.store.representation.AbstractDomain;
+
+public record PartialFunction<A, C>(String name, int arity, AbstractDomain<A, C> abstractDomain)
+                implements AnyPartialFunction, PartialSymbol<A, C> {
+        @Override
+        public A defaultValue() {
+                return null;
+        }
+
+        @Override
+        public C defaultConcreteValue() {
+                return null;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                return this == o;
+        }
+
+        @Override
+        public int hashCode() {
+                // Compare by identity to make hash table lookups more efficient.
+                return System.identityHashCode(this);
+        }
+
+        @Override
+        public String toString() {
+                return "%s/%d".formatted(name, arity);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialRelation.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialRelation.java
new file mode 100644
index 00000000..6b2f050b
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialRelation.java
@@ -0,0 +1,60 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.representation;
+
+import tools.refinery.store.query.Constraint;
+import tools.refinery.store.query.term.Parameter;
+import tools.refinery.store.representation.AbstractDomain;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.representation.TruthValueDomain;
+
+import java.util.Arrays;
+import java.util.List;
+
+public record PartialRelation(String name, int arity) implements PartialSymbol<TruthValue, Boolean>, Constraint {
+        @Override
+        public AbstractDomain<TruthValue, Boolean> abstractDomain() {
+                return TruthValueDomain.INSTANCE;
+        }
+
+        @Override
+        public TruthValue defaultValue() {
+                return TruthValue.FALSE;
+        }
+
+        @Override
+        public Boolean defaultConcreteValue() {
+                return false;
+        }
+
+        @Override
+        public List<Parameter> getParameters() {
+                var parameters = new Parameter[arity];
+                Arrays.fill(parameters, Parameter.NODE_OUT);
+                return List.of(parameters);
+        }
+
+        @Override
+        public String toReferenceString() {
+                return name;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                return this == o;
+        }
+
+        @Override
+        public int hashCode() {
+                // Compare by identity to make hash table lookups more efficient.
+                return System.identityHashCode(this);
+        }
+
+        @Override
+        public String toString() {
+                return "%s/%d".formatted(name, arity);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialSymbol.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialSymbol.java
new file mode 100644
index 00000000..3a08bdd8
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/representation/PartialSymbol.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.representation;
+
+import tools.refinery.store.representation.AbstractDomain;
+
+public sealed interface PartialSymbol<A, C> extends AnyPartialSymbol permits PartialFunction, PartialRelation {
+        @Override
+        AbstractDomain<A, C> abstractDomain();
+
+        A defaultValue();
+
+        C defaultConcreteValue();
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/Seed.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/Seed.java
new file mode 100644
index 00000000..08079f12
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/Seed.java
@@ -0,0 +1,19 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.seed;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+public interface Seed<T> {
+        int arity();
+
+        T reducedValue();
+
+        T get(Tuple key);
+
+        Cursor<Tuple, T> getCursor(T defaultValue, int nodeCount);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/UniformSeed.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/UniformSeed.java
new file mode 100644
index 00000000..451d1513
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/seed/UniformSeed.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.seed;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.tuple.Tuple;
+
+public record UniformSeed<T>(int arity, T reducedValue) implements Seed<T> {
+        public UniformSeed {
+                if (arity < 0) {
+                        throw new IllegalArgumentException("Arity must not be negative");
+                }
+        }
+
+        @Override
+        public T get(Tuple key) {
+                return reducedValue;
+        }
+
+        @Override
+        public Cursor<Tuple, T> getCursor(T defaultValue, int nodeCount) {
+                return null;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/Advice.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/Advice.java
new file mode 100644
index 00000000..d6a9e02c
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/Advice.java
@@ -0,0 +1,159 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator;
+
+import tools.refinery.store.query.substitution.Substitution;
+import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.literal.Literal;
+
+import java.util.*;
+
+public final class Advice {
+        private final AnyPartialSymbol source;
+        private final PartialRelation target;
+        private final AdviceSlot slot;
+        private final boolean mandatory;
+        private final List<Variable> parameters;
+        private final List<Literal> literals;
+        private boolean processed;
+
+        public Advice(AnyPartialSymbol source, PartialRelation target, AdviceSlot slot, boolean mandatory, List<Variable> parameters, List<Literal> literals) {
+                if (mandatory && !slot.isMonotonic()) {
+                        throw new IllegalArgumentException("Only monotonic advice can be mandatory");
+                }
+                this.source = source;
+                this.target = target;
+                this.slot = slot;
+                this.mandatory = mandatory;
+                checkArity(parameters);
+                this.parameters = parameters;
+                this.literals = literals;
+        }
+
+        public AnyPartialSymbol source() {
+                return source;
+        }
+
+        public PartialRelation target() {
+                return target;
+        }
+
+        public AdviceSlot slot() {
+                return slot;
+        }
+
+        public boolean mandatory() {
+                return mandatory;
+        }
+
+        public List<Variable> parameters() {
+                return parameters;
+        }
+
+        public List<Literal> literals() {
+                return literals;
+        }
+
+        public boolean processed() {
+                return processed;
+        }
+
+        public List<Literal> substitute(List<Variable> substituteParameters) {
+                checkArity(substituteParameters);
+                markProcessed();
+                // Use a renewing substitution to remove any non-parameter variables and avoid clashed between variables
+                // coming from different advice in the same clause.
+                var substitution = Substitution.builder().putManyChecked(parameters, substituteParameters).renewing().build();
+                return literals.stream().map(literal -> literal.substitute(substitution)).toList();
+        }
+
+        private void markProcessed() {
+                processed = true;
+        }
+
+        public void checkProcessed() {
+                if (mandatory && !processed) {
+                        throw new IllegalStateException("Mandatory advice %s was not processed".formatted(this));
+                }
+        }
+
+        private void checkArity(List<Variable> toCheck) {
+                if (toCheck.size() != target.arity()) {
+                        throw new IllegalArgumentException("%s needs %d parameters, but got %s".formatted(target.name(),
+                                        target.arity(), parameters.size()));
+                }
+        }
+
+        public static Builder builderFor(AnyPartialSymbol source, PartialRelation target, AdviceSlot slot) {
+                return new Builder(source, target, slot);
+        }
+
+
+        @Override
+        public String toString() {
+                return "Advice[source=%s, target=%s, slot=%s, mandatory=%s, parameters=%s, literals=%s]".formatted(source,
+                                target, slot, mandatory, parameters, literals);
+        }
+
+        public static class Builder {
+                private final AnyPartialSymbol source;
+                private final PartialRelation target;
+                private final AdviceSlot slot;
+                private boolean mandatory;
+                private final List<Variable> parameters = new ArrayList<>();
+                private final List<Literal> literals = new ArrayList<>();
+
+                private Builder(AnyPartialSymbol source, PartialRelation target, AdviceSlot slot) {
+                        this.source = source;
+                        this.target = target;
+                        this.slot = slot;
+                }
+
+                public Builder mandatory(boolean mandatory) {
+                        this.mandatory = mandatory;
+                        return this;
+                }
+
+                public Builder mandatory() {
+                        return mandatory(false);
+                }
+
+                public Builder parameters(List<Variable> variables) {
+                        parameters.addAll(variables);
+                        return this;
+                }
+
+                public Builder parameters(Variable... variables) {
+                        return parameters(List.of(variables));
+                }
+
+                public Builder parameter(Variable variable) {
+                        parameters.add(variable);
+                        return this;
+                }
+
+                public Builder literals(Collection<Literal> literals) {
+                        this.literals.addAll(literals);
+                        return this;
+                }
+
+                public Builder literals(Literal... literals) {
+                        return literals(List.of(literals));
+                }
+
+                public Builder literal(Literal literal) {
+                        literals.add(literal);
+                        return this;
+                }
+
+                public Advice build() {
+                        return new Advice(source, target, slot, mandatory, Collections.unmodifiableList(parameters),
+                                        Collections.unmodifiableList(literals));
+                }
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/AdviceSlot.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/AdviceSlot.java
new file mode 100644
index 00000000..bab20340
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/AdviceSlot.java
@@ -0,0 +1,30 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator;
+
+import tools.refinery.store.representation.TruthValue;
+
+public enum AdviceSlot {
+        EXTEND_MUST(true),
+
+        RESTRICT_MAY(true),
+
+        /**
+         * Same as {@link #RESTRICT_MAY}, but only active if the value of the relation is not {@link TruthValue#TRUE} or
+         * {@link TruthValue#ERROR}.
+         */
+        RESTRICT_NEW(false);
+
+        private final boolean monotonic;
+
+        AdviceSlot(boolean monotonic) {
+                this.monotonic = monotonic;
+        }
+
+        public boolean isMonotonic() {
+                return monotonic;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslatedRelation.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslatedRelation.java
new file mode 100644
index 00000000..4a5a8843
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslatedRelation.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.literal.CallPolarity;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.reasoning.PartialInterpretation;
+import tools.refinery.store.reasoning.literal.Modality;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.List;
+
+public interface TranslatedRelation {
+        PartialRelation getSource();
+
+        void configure(List<Advice> advices);
+
+        List<Literal> call(CallPolarity polarity, Modality modality, List<Variable> arguments);
+
+        PartialInterpretation<TruthValue, Boolean> createPartialInterpretation(Model model);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java
new file mode 100644
index 00000000..6e44a7d7
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java
@@ -0,0 +1,32 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.reasoning.ReasoningBuilder;
+
+import java.util.Collection;
+
+public abstract class TranslationUnit {
+        private ReasoningBuilder reasoningBuilder;
+
+        protected ReasoningBuilder getReasoningBuilder() {
+                return reasoningBuilder;
+        }
+
+        public void setPartialInterpretationBuilder(ReasoningBuilder reasoningBuilder) {
+                this.reasoningBuilder = reasoningBuilder;
+                configureReasoningBuilder();
+        }
+
+        protected void configureReasoningBuilder() {
+                // Nothing to configure by default.
+        }
+
+        public abstract Collection<TranslatedRelation> getTranslatedRelations();
+
+        public abstract void initializeModel(Model model, int nodeCount);
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionInterpretation.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionInterpretation.java
new file mode 100644
index 00000000..2a151aa2
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionInterpretation.java
@@ -0,0 +1,93 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.base;
+
+import tools.refinery.store.map.Cursor;
+import tools.refinery.store.model.Interpretation;
+import tools.refinery.store.query.resultset.ResultSet;
+import tools.refinery.store.reasoning.MergeResult;
+import tools.refinery.store.reasoning.PartialInterpretation;
+import tools.refinery.store.reasoning.ReasoningAdapter;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.representation.TruthValue;
+import tools.refinery.store.tuple.Tuple;
+
+public class BaseDecisionInterpretation implements PartialInterpretation<TruthValue, Boolean> {
+        private final ReasoningAdapter reasoningAdapter;
+        private PartialRelation partialRelation;
+        private final ResultSet<Boolean> mustResultSet;
+        private final ResultSet<Boolean> mayResultSet;
+        private final ResultSet<Boolean> errorResultSet;
+        private final ResultSet<Boolean> currentResultSet;
+        private final Interpretation<TruthValue> interpretation;
+
+        public BaseDecisionInterpretation(ReasoningAdapter reasoningAdapter, ResultSet<Boolean> mustResultSet,
+                                                                          ResultSet<Boolean> mayResultSet, ResultSet<Boolean> errorResultSet,
+                                                                          ResultSet<Boolean> currentResultSet, Interpretation<TruthValue> interpretation) {
+                this.reasoningAdapter = reasoningAdapter;
+                this.mustResultSet = mustResultSet;
+                this.mayResultSet = mayResultSet;
+                this.errorResultSet = errorResultSet;
+                this.currentResultSet = currentResultSet;
+                this.interpretation = interpretation;
+        }
+
+        @Override
+        public ReasoningAdapter getAdapter() {
+                return reasoningAdapter;
+        }
+
+        @Override
+        public int countUnfinished() {
+                return 0;
+        }
+
+        @Override
+        public int countErrors() {
+                return errorResultSet.size();
+        }
+
+        @Override
+        public PartialRelation getPartialSymbol() {
+                return partialRelation;
+        }
+
+        @Override
+        public TruthValue get(Tuple key) {
+                return null;
+        }
+
+        @Override
+        public Cursor<Tuple, TruthValue> getAll() {
+                return null;
+        }
+
+        @Override
+        public MergeResult merge(Tuple key, TruthValue value) {
+                TruthValue newValue;
+                switch (value) {
+                case UNKNOWN -> {
+                        return MergeResult.UNCHANGED;
+                }
+                case TRUE -> newValue = mayResultSet.get(key) ? TruthValue.TRUE : TruthValue.ERROR;
+                case FALSE -> newValue = mustResultSet.get(key) ? TruthValue.ERROR : TruthValue.FALSE;
+                case ERROR -> newValue = TruthValue.ERROR;
+                default -> throw new IllegalArgumentException("Unknown truth value: " + value);
+                }
+                var oldValue = interpretation.put(key, newValue);
+                return oldValue == TruthValue.ERROR ? MergeResult.UNCHANGED : MergeResult.REFINED;
+        }
+
+        @Override
+        public Boolean getConcrete(Tuple key) {
+                return currentResultSet.get(key);
+        }
+
+        @Override
+        public Cursor<Tuple, Boolean> getAllConcrete() {
+                return null;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java
new file mode 100644
index 00000000..a1e4b816
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java
@@ -0,0 +1,49 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.base;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.reasoning.seed.Seed;
+import tools.refinery.store.reasoning.seed.UniformSeed;
+import tools.refinery.store.reasoning.translator.TranslatedRelation;
+import tools.refinery.store.reasoning.translator.TranslationUnit;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.Collection;
+import java.util.List;
+
+public class BaseDecisionTranslationUnit extends TranslationUnit {
+        private final PartialRelation partialRelation;
+        private final Seed<TruthValue> seed;
+        private final Symbol<TruthValue> symbol;
+
+        public BaseDecisionTranslationUnit(PartialRelation partialRelation, Seed<TruthValue> seed) {
+                if (seed.arity() != partialRelation.arity()) {
+                        throw new IllegalArgumentException("Expected seed with arity %d for %s, got arity %s"
+                                        .formatted(partialRelation.arity(), partialRelation, seed.arity()));
+                }
+                this.partialRelation = partialRelation;
+                this.seed = seed;
+                symbol = Symbol.of(partialRelation.name(), partialRelation.arity(), TruthValue.class, TruthValue.UNKNOWN);
+        }
+
+        public BaseDecisionTranslationUnit(PartialRelation partialRelation) {
+                this(partialRelation, new UniformSeed<>(partialRelation.arity(), TruthValue.UNKNOWN));
+        }
+
+        @Override
+        public Collection<TranslatedRelation> getTranslatedRelations() {
+                return List.of(new TranslatedBaseDecision(getReasoningBuilder(), partialRelation, symbol));
+        }
+
+        @Override
+        public void initializeModel(Model model, int nodeCount) {
+                var interpretation = model.getInterpretation(symbol);
+                interpretation.putAll(seed.getCursor(TruthValue.UNKNOWN, nodeCount));
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/TranslatedBaseDecision.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/TranslatedBaseDecision.java
new file mode 100644
index 00000000..4782eb46
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/TranslatedBaseDecision.java
@@ -0,0 +1,54 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.base;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.Variable;
+import tools.refinery.store.query.literal.CallPolarity;
+import tools.refinery.store.query.literal.Literal;
+import tools.refinery.store.reasoning.PartialInterpretation;
+import tools.refinery.store.reasoning.ReasoningBuilder;
+import tools.refinery.store.reasoning.literal.Modality;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.reasoning.translator.Advice;
+import tools.refinery.store.reasoning.translator.TranslatedRelation;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.List;
+
+class TranslatedBaseDecision implements TranslatedRelation {
+        private final ReasoningBuilder reasoningBuilder;
+        private final PartialRelation partialRelation;
+        private final Symbol<TruthValue> symbol;
+
+        public TranslatedBaseDecision(ReasoningBuilder reasoningBuilder, PartialRelation partialRelation,
+                                                                  Symbol<TruthValue> symbol) {
+                this.reasoningBuilder = reasoningBuilder;
+                this.partialRelation = partialRelation;
+                this.symbol = symbol;
+        }
+
+        @Override
+        public PartialRelation getSource() {
+                return partialRelation;
+        }
+
+        @Override
+        public void configure(List<Advice> advices) {
+
+        }
+
+        @Override
+        public List<Literal> call(CallPolarity polarity, Modality modality, List<Variable> arguments) {
+                return null;
+        }
+
+        @Override
+        public PartialInterpretation<TruthValue, Boolean> createPartialInterpretation(Model model) {
+                return null;
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/EliminatedType.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/EliminatedType.java
new file mode 100644
index 00000000..6e4728db
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/EliminatedType.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+record EliminatedType(PartialRelation replacement) implements TypeAnalysisResult {
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/ExtendedTypeInfo.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/ExtendedTypeInfo.java
new file mode 100644
index 00000000..7a917dcf
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/ExtendedTypeInfo.java
@@ -0,0 +1,106 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import org.jetbrains.annotations.NotNull;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.Objects;
+import java.util.Set;
+
+final class ExtendedTypeInfo implements Comparable<ExtendedTypeInfo> {
+        private final int index;
+        private final PartialRelation type;
+        private final TypeInfo typeInfo;
+        private final Set<PartialRelation> allSubtypes = new LinkedHashSet<>();
+        private final Set<PartialRelation> allSupertypes;
+        private final Set<PartialRelation> concreteSubtypesAndSelf = new LinkedHashSet<>();
+        private Set<PartialRelation> directSubtypes;
+        private final Set<PartialRelation> unsortedDirectSupertypes = new HashSet<>();
+
+        public ExtendedTypeInfo(int index, PartialRelation type, TypeInfo typeInfo) {
+                this.index = index;
+                this.type = type;
+                this.typeInfo = typeInfo;
+                this.allSupertypes = new LinkedHashSet<>(typeInfo.supertypes());
+        }
+
+        public PartialRelation getType() {
+                return type;
+        }
+
+        public TypeInfo getTypeInfo() {
+                return typeInfo;
+        }
+
+        public boolean isAbstractType() {
+                return getTypeInfo().abstractType();
+        }
+
+        public Set<PartialRelation> getAllSubtypes() {
+                return allSubtypes;
+        }
+
+        public Set<PartialRelation> getAllSupertypes() {
+                return allSupertypes;
+        }
+
+        public Set<PartialRelation> getAllSupertypesAndSelf() {
+                var allSubtypesAndSelf = new HashSet<PartialRelation>(allSupertypes.size() + 1);
+                addMust(allSubtypesAndSelf);
+                return allSubtypesAndSelf;
+        }
+
+        public Set<PartialRelation> getConcreteSubtypesAndSelf() {
+                return concreteSubtypesAndSelf;
+        }
+
+        public Set<PartialRelation> getDirectSubtypes() {
+                return directSubtypes;
+        }
+
+        public Set<PartialRelation> getUnsortedDirectSupertypes() {
+                return unsortedDirectSupertypes;
+        }
+
+        public void setDirectSubtypes(Set<PartialRelation> directSubtypes) {
+                this.directSubtypes = directSubtypes;
+        }
+
+        public boolean allowsAllConcreteTypes(Set<PartialRelation> concreteTypes) {
+                for (var concreteType : concreteTypes) {
+                        if (!concreteSubtypesAndSelf.contains(concreteType)) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+
+        public void addMust(Set<PartialRelation> mustTypes) {
+                mustTypes.add(type);
+                mustTypes.addAll(allSupertypes);
+        }
+
+        @Override
+        public int compareTo(@NotNull ExtendedTypeInfo extendedTypeInfo) {
+                return Integer.compare(index, extendedTypeInfo.index);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                ExtendedTypeInfo that = (ExtendedTypeInfo) o;
+                return index == that.index;
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(index);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMayTypeView.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMayTypeView.java
new file mode 100644
index 00000000..40de4644
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMayTypeView.java
@@ -0,0 +1,40 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.query.view.TuplePreservingView;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Objects;
+
+class InferredMayTypeView extends TuplePreservingView<InferredType> {
+        private final PartialRelation type;
+
+        InferredMayTypeView(PartialRelation type) {
+                super(TypeHierarchyTranslationUnit.INFERRED_TYPE_SYMBOL, "%s#may".formatted(type));
+                this.type = type;
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, InferredType value) {
+                return value.mayConcreteTypes().contains(type);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                InferredMayTypeView that = (InferredMayTypeView) o;
+                return Objects.equals(type, that.type);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), type);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMustTypeView.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMustTypeView.java
new file mode 100644
index 00000000..1a121547
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredMustTypeView.java
@@ -0,0 +1,40 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.query.view.TuplePreservingView;
+import tools.refinery.store.tuple.Tuple;
+
+import java.util.Objects;
+
+class InferredMustTypeView extends TuplePreservingView<InferredType> {
+        private final PartialRelation type;
+
+        InferredMustTypeView(PartialRelation type) {
+                super(TypeHierarchyTranslationUnit.INFERRED_TYPE_SYMBOL, "%s#must".formatted(type));
+                this.type = type;
+        }
+
+        @Override
+        protected boolean doFilter(Tuple key, InferredType value) {
+                return value.mustTypes().contains(type);
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                if (!super.equals(o)) return false;
+                InferredMustTypeView that = (InferredMustTypeView) o;
+                return Objects.equals(type, that.type);
+        }
+
+        @Override
+        public int hashCode() {
+                return Objects.hash(super.hashCode(), type);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredType.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredType.java
new file mode 100644
index 00000000..fd05158b
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredType.java
@@ -0,0 +1,35 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import java.util.Collections;
+import java.util.Set;
+
+record InferredType(Set<PartialRelation> mustTypes, Set<PartialRelation> mayConcreteTypes,
+                                        PartialRelation currentType) {
+        public static final InferredType UNTYPED = new InferredType(Set.of(), Set.of(), null);
+
+        public InferredType(Set<PartialRelation> mustTypes, Set<PartialRelation> mayConcreteTypes,
+                                                PartialRelation currentType) {
+                this.mustTypes = Collections.unmodifiableSet(mustTypes);
+                this.mayConcreteTypes = Collections.unmodifiableSet(mayConcreteTypes);
+                this.currentType = currentType;
+        }
+
+        public boolean isConsistent() {
+                return currentType != null || mustTypes.isEmpty();
+        }
+
+        public boolean isMust(PartialRelation partialRelation) {
+                return mustTypes.contains(partialRelation);
+        }
+
+        public boolean isMayConcrete(PartialRelation partialRelation) {
+                return mayConcreteTypes.contains(partialRelation);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/PreservedType.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/PreservedType.java
new file mode 100644
index 00000000..0696f4c3
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/PreservedType.java
@@ -0,0 +1,141 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.*;
+
+final class PreservedType implements TypeAnalysisResult {
+        private final ExtendedTypeInfo extendedTypeInfo;
+        private final List<PartialRelation> directSubtypes;
+        private final List<ExtendedTypeInfo> allExternalTypeInfoList;
+        private final InferredType inferredType;
+
+        public PreservedType(ExtendedTypeInfo extendedTypeInfo, List<ExtendedTypeInfo> allExternalTypeInfoList) {
+                this.extendedTypeInfo = extendedTypeInfo;
+                directSubtypes = List.copyOf(extendedTypeInfo.getDirectSubtypes());
+                this.allExternalTypeInfoList = allExternalTypeInfoList;
+                inferredType = propagateMust(extendedTypeInfo.getAllSupertypesAndSelf(),
+                                extendedTypeInfo.getConcreteSubtypesAndSelf());
+        }
+
+        public PartialRelation type() {
+                return extendedTypeInfo.getType();
+        }
+
+        public List<PartialRelation> getDirectSubtypes() {
+                return directSubtypes;
+        }
+
+        public boolean isAbstractType() {
+                return extendedTypeInfo.isAbstractType();
+        }
+
+        public boolean isVacuous() {
+                return isAbstractType() && directSubtypes.isEmpty();
+        }
+
+        public InferredType asInferredType() {
+                return inferredType;
+        }
+
+        public InferredType merge(InferredType inferredType, TruthValue value) {
+                return switch (value) {
+                        case UNKNOWN -> inferredType;
+                        case TRUE -> addMust(inferredType);
+                        case FALSE -> removeMay(inferredType);
+                        case ERROR -> addError(inferredType);
+                };
+        }
+
+        private InferredType addMust(InferredType inferredType) {
+                var originalMustTypes = inferredType.mustTypes();
+                if (originalMustTypes.contains(type())) {
+                        return inferredType;
+                }
+                var mustTypes = new HashSet<>(originalMustTypes);
+                extendedTypeInfo.addMust(mustTypes);
+                var originalMayConcreteTypes = inferredType.mayConcreteTypes();
+                var mayConcreteTypes = new LinkedHashSet<>(originalMayConcreteTypes);
+                Set<PartialRelation> mayConcreteTypesResult;
+                if (mayConcreteTypes.retainAll(extendedTypeInfo.getConcreteSubtypesAndSelf())) {
+                        mayConcreteTypesResult = mayConcreteTypes;
+                } else {
+                        mayConcreteTypesResult = originalMayConcreteTypes;
+                }
+                return propagateMust(mustTypes, mayConcreteTypesResult);
+        }
+
+        private InferredType removeMay(InferredType inferredType) {
+                var originalMayConcreteTypes = inferredType.mayConcreteTypes();
+                var mayConcreteTypes = new LinkedHashSet<>(originalMayConcreteTypes);
+                if (!mayConcreteTypes.removeAll(extendedTypeInfo.getConcreteSubtypesAndSelf())) {
+                        return inferredType;
+                }
+                return propagateMust(inferredType.mustTypes(), mayConcreteTypes);
+        }
+
+        private InferredType addError(InferredType inferredType) {
+                var originalMustTypes = inferredType.mustTypes();
+                if (originalMustTypes.contains(type())) {
+                        if (inferredType.mayConcreteTypes().isEmpty()) {
+                                return inferredType;
+                        }
+                        return new InferredType(originalMustTypes, Set.of(), null);
+                }
+                var mustTypes = new HashSet<>(originalMustTypes);
+                extendedTypeInfo.addMust(mustTypes);
+                return new InferredType(mustTypes, Set.of(), null);
+        }
+
+        private InferredType propagateMust(Set<PartialRelation> originalMustTypes,
+                                                                           Set<PartialRelation> mayConcreteTypes) {
+                // It is possible that there is not type at all, do not force one by propagation.
+                var maybeUntyped = originalMustTypes.isEmpty();
+                // Para-consistent case, do not propagate must types to avoid logical explosion.
+                var paraConsistentOrSurelyUntyped = mayConcreteTypes.isEmpty();
+                if (maybeUntyped || paraConsistentOrSurelyUntyped) {
+                        return new InferredType(originalMustTypes, mayConcreteTypes, null);
+                }
+                var currentType = computeCurrentType(mayConcreteTypes);
+                var mustTypes = new HashSet<>(originalMustTypes);
+                boolean changed = false;
+                for (var newMustExtendedTypeInfo : allExternalTypeInfoList) {
+                        var newMustType = newMustExtendedTypeInfo.getType();
+                        if (mustTypes.contains(newMustType)) {
+                                continue;
+                        }
+                        if (newMustExtendedTypeInfo.allowsAllConcreteTypes(mayConcreteTypes)) {
+                                newMustExtendedTypeInfo.addMust(mustTypes);
+                                changed = true;
+                        }
+                }
+                if (!changed) {
+                        return new InferredType(originalMustTypes, mayConcreteTypes, currentType);
+                }
+                return new InferredType(mustTypes, mayConcreteTypes, currentType);
+        }
+
+        /**
+         * Returns a concrete type that is allowed by a (consistent, i.e., nonempty) set of <b>may</b> concrete types.
+         *
+         * @param mayConcreteTypes The set of allowed concrete types. Must not be empty.
+         * @return The first concrete type that is allowed by {@code matConcreteTypes}.
+         */
+        private PartialRelation computeCurrentType(Set<PartialRelation> mayConcreteTypes) {
+                for (var concreteExtendedTypeInfo : allExternalTypeInfoList) {
+                        var concreteType = concreteExtendedTypeInfo.getType();
+                        if (!concreteExtendedTypeInfo.isAbstractType() && mayConcreteTypes.contains(concreteType)) {
+                                return concreteType;
+                        }
+                }
+                // We have already filtered out the para-consistent case in {@link #propagateMust(Set<PartialRelation>,
+                // Set<PartialRelation>}.
+                throw new AssertionError("No concrete type in %s".formatted(mayConcreteTypes));
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalysisResult.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalysisResult.java
new file mode 100644
index 00000000..fbf8a7c9
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalysisResult.java
@@ -0,0 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+sealed interface TypeAnalysisResult permits EliminatedType, PreservedType {
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzer.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzer.java
new file mode 100644
index 00000000..e97ce954
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzer.java
@@ -0,0 +1,207 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import java.util.*;
+
+class TypeAnalyzer {
+        private final Map<PartialRelation, ExtendedTypeInfo> extendedTypeInfoMap;
+        private final Map<PartialRelation, PartialRelation> replacements = new LinkedHashMap<>();
+        private final InferredType unknownType;
+        private final Map<PartialRelation, TypeAnalysisResult> analysisResults;
+
+        public TypeAnalyzer(Map<PartialRelation, TypeInfo> typeInfoMap) {
+                int size = typeInfoMap.size();
+                extendedTypeInfoMap = new LinkedHashMap<>(size);
+                var concreteTypes = new LinkedHashSet<PartialRelation>();
+                int index = 0;
+                for (var entry : typeInfoMap.entrySet()) {
+                        var type = entry.getKey();
+                        var typeInfo = entry.getValue();
+                        extendedTypeInfoMap.put(type, new ExtendedTypeInfo(index, type, typeInfo));
+                        if (!typeInfo.abstractType()) {
+                                concreteTypes.add(type);
+                        }
+                        index++;
+                }
+                unknownType = new InferredType(Set.of(), concreteTypes, null);
+                computeAllSupertypes();
+                computeAllAndConcreteSubtypes();
+                computeDirectSubtypes();
+                eliminateTrivialSupertypes();
+                analysisResults = computeAnalysisResults();
+        }
+
+        public InferredType getUnknownType() {
+                return unknownType;
+        }
+
+        public Map<PartialRelation, TypeAnalysisResult> getAnalysisResults() {
+                return analysisResults;
+        }
+
+        private void computeAllSupertypes() {
+                boolean changed;
+                do {
+                        changed = false;
+                        for (var extendedTypeInfo : extendedTypeInfoMap.values()) {
+                                var found = new HashSet<PartialRelation>();
+                                var allSupertypes = extendedTypeInfo.getAllSupertypes();
+                                for (var supertype : allSupertypes) {
+                                        found.addAll(extendedTypeInfoMap.get(supertype).getAllSupertypes());
+                                }
+                                if (allSupertypes.addAll(found)) {
+                                        changed = true;
+                                }
+                        }
+                } while (changed);
+        }
+
+        private void computeAllAndConcreteSubtypes() {
+                for (var extendedTypeInfo : extendedTypeInfoMap.values()) {
+                        var type = extendedTypeInfo.getType();
+                        if (!extendedTypeInfo.isAbstractType()) {
+                                extendedTypeInfo.getConcreteSubtypesAndSelf().add(type);
+                        }
+                        for (var supertype : extendedTypeInfo.getAllSupertypes()) {
+                                if (type.equals(supertype)) {
+                                        throw new IllegalArgumentException("%s cannot be a supertype of itself".formatted(type));
+                                }
+                                var supertypeInfo = extendedTypeInfoMap.get(supertype);
+                                supertypeInfo.getAllSubtypes().add(type);
+                                if (!extendedTypeInfo.isAbstractType()) {
+                                        supertypeInfo.getConcreteSubtypesAndSelf().add(type);
+                                }
+                        }
+                }
+        }
+
+        private void computeDirectSubtypes() {
+                for (var extendedTypeInfo : extendedTypeInfoMap.values()) {
+                        var allSubtypes = extendedTypeInfo.getAllSubtypes();
+                        var directSubtypes = new LinkedHashSet<>(allSubtypes);
+                        var indirectSubtypes = new LinkedHashSet<PartialRelation>(allSubtypes.size());
+                        for (var subtype : allSubtypes) {
+                                indirectSubtypes.addAll(extendedTypeInfoMap.get(subtype).getAllSubtypes());
+                        }
+                        directSubtypes.removeAll(indirectSubtypes);
+                        extendedTypeInfo.setDirectSubtypes(directSubtypes);
+                }
+        }
+
+        private void eliminateTrivialSupertypes() {
+                boolean changed;
+                do {
+                        var toRemove = new ArrayList<PartialRelation>();
+                        for (var entry : extendedTypeInfoMap.entrySet()) {
+                                var extendedTypeInfo = entry.getValue();
+                                boolean isAbstract = extendedTypeInfo.isAbstractType();
+                                // Do not eliminate abstract types with 0 subtypes, because they can be used para-consistently, i.e.,
+                                // an object determined to <b>must</b> have an abstract type with 0 subtypes <b>may not</b> ever exist.
+                                boolean hasSingleDirectSubtype = extendedTypeInfo.getDirectSubtypes().size() == 1;
+                                if (isAbstract && hasSingleDirectSubtype) {
+                                        toRemove.add(entry.getKey());
+                                }
+                        }
+                        toRemove.forEach(this::removeTrivialType);
+                        changed = !toRemove.isEmpty();
+                } while (changed);
+        }
+
+        private void removeTrivialType(PartialRelation trivialType) {
+                var extendedTypeInfo = extendedTypeInfoMap.get(trivialType);
+                var iterator = extendedTypeInfo.getDirectSubtypes().iterator();
+                if (!iterator.hasNext()) {
+                        throw new AssertionError("Expected trivial supertype %s to have a direct subtype"
+                                        .formatted(trivialType));
+                }
+                PartialRelation replacement = setReplacement(trivialType, iterator.next());
+                if (iterator.hasNext()) {
+                        throw new AssertionError("Expected trivial supertype %s to have at most 1 direct subtype"
+                                        .formatted(trivialType));
+                }
+                replacements.put(trivialType, replacement);
+                for (var supertype : extendedTypeInfo.getAllSupertypes()) {
+                        var extendedSupertypeInfo = extendedTypeInfoMap.get(supertype);
+                        if (!extendedSupertypeInfo.getAllSubtypes().remove(trivialType)) {
+                                throw new AssertionError("Expected %s to be subtype of %s".formatted(trivialType, supertype));
+                        }
+                        var directSubtypes = extendedSupertypeInfo.getDirectSubtypes();
+                        if (directSubtypes.remove(trivialType)) {
+                                directSubtypes.add(replacement);
+                        }
+                }
+                for (var subtype : extendedTypeInfo.getAllSubtypes()) {
+                        var extendedSubtypeInfo = extendedTypeInfoMap.get(subtype);
+                        if (!extendedSubtypeInfo.getAllSupertypes().remove(trivialType)) {
+                                throw new AssertionError("Expected %s to be supertype of %s".formatted(trivialType, subtype));
+                        }
+                }
+                extendedTypeInfoMap.remove(trivialType);
+        }
+
+        private PartialRelation setReplacement(PartialRelation trivialRelation, PartialRelation replacement) {
+                if (replacement == null) {
+                        return trivialRelation;
+                }
+                var resolved = setReplacement(replacement, replacements.get(replacement));
+                replacements.put(trivialRelation, resolved);
+                return resolved;
+        }
+
+        private Map<PartialRelation, TypeAnalysisResult> computeAnalysisResults() {
+                var allExtendedTypeInfoList = sortTypes();
+                var results = new LinkedHashMap<PartialRelation, TypeAnalysisResult>(
+                                allExtendedTypeInfoList.size() + replacements.size());
+                for (var extendedTypeInfo : allExtendedTypeInfoList) {
+                        var type = extendedTypeInfo.getType();
+                        results.put(type, new PreservedType(extendedTypeInfo, allExtendedTypeInfoList));
+                }
+                for (var entry : replacements.entrySet()) {
+                        var type = entry.getKey();
+                        results.put(type, new EliminatedType(entry.getValue()));
+                }
+                return Collections.unmodifiableMap(results);
+        }
+
+        private List<ExtendedTypeInfo> sortTypes() {
+                // Invert {@code directSubtypes} to keep track of the out-degree of types.
+                for (var extendedTypeInfo : extendedTypeInfoMap.values()) {
+                        for (var directSubtype : extendedTypeInfo.getDirectSubtypes()) {
+                                var extendedDirectSubtypeInfo = extendedTypeInfoMap.get(directSubtype);
+                                extendedDirectSubtypeInfo.getUnsortedDirectSupertypes().add(extendedTypeInfo.getType());
+                        }
+                }
+                // Build a <i>inverse</i> topological order ({@code extends} edges always points to earlier nodes in the order,
+                // breaking ties according to the original order ({@link ExtendedTypeInfo#index}) to form a 'stable' sort.
+                // See, e.g., https://stackoverflow.com/a/11236027.
+                var priorityQueue = new PriorityQueue<ExtendedTypeInfo>();
+                for (var extendedTypeInfo : extendedTypeInfoMap.values()) {
+                        if (extendedTypeInfo.getUnsortedDirectSupertypes().isEmpty()) {
+                                priorityQueue.add(extendedTypeInfo);
+                        }
+                }
+                var sorted = new ArrayList<ExtendedTypeInfo>(extendedTypeInfoMap.size());
+                while (!priorityQueue.isEmpty()) {
+                        var extendedTypeInfo = priorityQueue.remove();
+                        sorted.add(extendedTypeInfo);
+                        for (var directSubtype : extendedTypeInfo.getDirectSubtypes()) {
+                                var extendedDirectSubtypeInfo = extendedTypeInfoMap.get(directSubtype);
+                                var unsortedDirectSupertypes = extendedDirectSubtypeInfo.getUnsortedDirectSupertypes();
+                                if (!unsortedDirectSupertypes.remove(extendedTypeInfo.getType())) {
+                                        throw new AssertionError("Expected %s to be a direct supertype of %s"
+                                                        .formatted(extendedTypeInfo.getType(), directSubtype));
+                                }
+                                if (unsortedDirectSupertypes.isEmpty()) {
+                                        priorityQueue.add(extendedDirectSubtypeInfo);
+                                }
+                        }
+                }
+                return Collections.unmodifiableList(sorted);
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyTranslationUnit.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyTranslationUnit.java
new file mode 100644
index 00000000..06e3c05f
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyTranslationUnit.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.model.Model;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.reasoning.translator.TranslatedRelation;
+import tools.refinery.store.reasoning.translator.TranslationUnit;
+import tools.refinery.store.representation.Symbol;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+public class TypeHierarchyTranslationUnit extends TranslationUnit {
+        static final Symbol<InferredType> INFERRED_TYPE_SYMBOL = Symbol.of(
+                        "inferredType", 1, InferredType.class, InferredType.UNTYPED);
+
+        private final TypeAnalyzer typeAnalyzer;
+
+        public TypeHierarchyTranslationUnit(Map<PartialRelation, TypeInfo> typeInfoMap) {
+                typeAnalyzer = new TypeAnalyzer(typeInfoMap);
+        }
+
+        @Override
+        public Collection<TranslatedRelation> getTranslatedRelations() {
+                return List.of();
+        }
+
+        @Override
+        public void initializeModel(Model model, int nodeCount) {
+
+        }
+}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeInfo.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeInfo.java
new file mode 100644
index 00000000..9f897e46
--- /dev/null
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeInfo.java
@@ -0,0 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import java.util.*;
+
+public record TypeInfo(Collection<PartialRelation> supertypes, boolean abstractType) {
+        public static Builder builder() {
+                return new Builder();
+        }
+
+        public static class Builder {
+                private final Set<PartialRelation> supertypes = new LinkedHashSet<>();
+                private boolean abstractType;
+
+                private Builder() {
+                }
+
+                public Builder supertypes(Collection<PartialRelation> supertypes) {
+                        this.supertypes.addAll(supertypes);
+                        return this;
+                }
+
+                public Builder supertypes(PartialRelation... supertypes) {
+                        return supertypes(List.of(supertypes));
+                }
+
+                public Builder supertype(PartialRelation supertype) {
+                        supertypes.add(supertype);
+                        return this;
+                }
+
+                public Builder abstractType(boolean abstractType) {
+                        this.abstractType = abstractType;
+                        return this;
+                }
+
+                public Builder abstractType() {
+                        return abstractType(true);
+                }
+
+                public TypeInfo build() {
+                        return new TypeInfo(Collections.unmodifiableSet(supertypes), abstractType);
+                }
+        }
+}
diff --git a/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredTypeTest.java b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredTypeTest.java
new file mode 100644
index 00000000..1d76855c
--- /dev/null
+++ b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/InferredTypeTest.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+
+class InferredTypeTest {
+        private final PartialRelation c1 = new PartialRelation("C1", 1);
+        private final PartialRelation c2 = new PartialRelation("C2", 1);
+
+        @Test
+        void untypedIsConsistentTest() {
+                var sut = new InferredType(Set.of(), Set.of(c1, c2), null);
+                assertThat(sut.isConsistent(), is(true));
+        }
+
+        @Test
+        void typedIsConsistentTest() {
+                var sut = new InferredType(Set.of(c1), Set.of(c1, c2), c1);
+                assertThat(sut.isConsistent(), is(true));
+        }
+
+        @Test
+        void typedIsInconsistentTest() {
+                var sut = new InferredType(Set.of(c1), Set.of(), null);
+                assertThat(sut.isConsistent(), is(false));
+        }
+}
diff --git a/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerExampleHierarchyTest.java b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerExampleHierarchyTest.java
new file mode 100644
index 00000000..05a476c6
--- /dev/null
+++ b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerExampleHierarchyTest.java
@@ -0,0 +1,208 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.LinkedHashMap;
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static org.junit.jupiter.api.Assertions.assertAll;
+
+class TypeAnalyzerExampleHierarchyTest {
+        private final PartialRelation a1 = new PartialRelation("A1", 1);
+        private final PartialRelation a2 = new PartialRelation("A2", 1);
+        private final PartialRelation a3 = new PartialRelation("A3", 1);
+        private final PartialRelation a4 = new PartialRelation("A4", 1);
+        private final PartialRelation a5 = new PartialRelation("A5", 1);
+        private final PartialRelation c1 = new PartialRelation("C1", 1);
+        private final PartialRelation c2 = new PartialRelation("C2", 1);
+        private final PartialRelation c3 = new PartialRelation("C3", 1);
+        private final PartialRelation c4 = new PartialRelation("C4", 1);
+
+        private TypeAnalyzer sut;
+        private TypeAnalyzerTester tester;
+
+        @BeforeEach
+        void beforeEach() {
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(a1, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(a2, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(a3, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(a4, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(a5, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(c1, TypeInfo.builder().supertypes(a1, a4).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertypes(a1, a2, a3, a4).build());
+                typeInfoMap.put(c3, TypeInfo.builder().supertype(a3).build());
+                typeInfoMap.put(c4, TypeInfo.builder().supertype(a4).build());
+                sut = new TypeAnalyzer(typeInfoMap);
+                tester = new TypeAnalyzerTester(sut);
+        }
+
+        @Test
+        void analysisResultsTest() {
+                assertAll(
+                                () -> tester.assertAbstractType(a1, c1, c2),
+                                () -> tester.assertEliminatedType(a2, c2),
+                                () -> tester.assertAbstractType(a3, c2, c3),
+                                () -> tester.assertAbstractType(a4, c1, c2, c4),
+                                () -> tester.assertVacuousType(a5),
+                                () -> tester.assertConcreteType(c1),
+                                () -> tester.assertConcreteType(c2),
+                                () -> tester.assertConcreteType(c3),
+                                () -> tester.assertConcreteType(c4)
+                );
+        }
+
+        @Test
+        void inferredTypesTest() {
+                assertAll(
+                                () -> assertThat(sut.getUnknownType(), is(new InferredType(Set.of(), Set.of(c1, c2, c3, c4), null))),
+                                () -> assertThat(tester.getInferredType(a1), is(new InferredType(Set.of(a1, a4), Set.of(c1, c2), c1))),
+                                () -> assertThat(tester.getInferredType(a3), is(new InferredType(Set.of(a3), Set.of(c2, c3), c2))),
+                                () -> assertThat(tester.getInferredType(a4), is(new InferredType(Set.of(a4), Set.of(c1, c2, c4), c1))),
+                                () -> assertThat(tester.getInferredType(a5), is(new InferredType(Set.of(a5), Set.of(), null))),
+                                () -> assertThat(tester.getInferredType(c1), is(new InferredType(Set.of(a1, a4, c1), Set.of(c1), c1))),
+                                () -> assertThat(tester.getInferredType(c2),
+                                                is(new InferredType(Set.of(a1, a3, a4, c2), Set.of(c2), c2))),
+                                () -> assertThat(tester.getInferredType(c3), is(new InferredType(Set.of(a3, c3), Set.of(c3), c3))),
+                                () -> assertThat(tester.getInferredType(c4), is(new InferredType(Set.of(a4, c4), Set.of(c4), c4)))
+                );
+        }
+
+        @Test
+        void consistentMustTest() {
+                var a1Result = tester.getPreservedType(a1);
+                var a3Result = tester.getPreservedType(a3);
+                var expected = new InferredType(Set.of(a1, a3, a4, c2), Set.of(c2), c2);
+                assertAll(
+                                () -> assertThat(a1Result.merge(a3Result.asInferredType(), TruthValue.TRUE), is(expected)),
+                                () -> assertThat(a3Result.merge(a1Result.asInferredType(), TruthValue.TRUE), is(expected)),
+                                () -> assertThat(a1Result.merge(sut.getUnknownType(), TruthValue.TRUE), is(a1Result.asInferredType())),
+                                () -> assertThat(a3Result.merge(sut.getUnknownType(), TruthValue.TRUE), is(a3Result.asInferredType())),
+                                () -> assertThat(a1Result.merge(a1Result.asInferredType(), TruthValue.TRUE),
+                                                is(a1Result.asInferredType()))
+                );
+        }
+
+        @Test
+        void consistentMayNotTest() {
+                var a1Result = tester.getPreservedType(a1);
+                var a3Result = tester.getPreservedType(a3);
+                var a4Result = tester.getPreservedType(a4);
+                assertAll(
+                                () -> assertThat(a1Result.merge(a3Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a3, c3), Set.of(c3), c3))),
+                                () -> assertThat(a3Result.merge(a1Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a1, a4, c1), Set.of(c1), c1))),
+                                () -> assertThat(a4Result.merge(a3Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a3, c3), Set.of(c3), c3))),
+                                () -> assertThat(a3Result.merge(a4Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a4), Set.of(c1, c4), c1))),
+                                () -> assertThat(a1Result.merge(sut.getUnknownType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(), Set.of(c3, c4), null))),
+                                () -> assertThat(a3Result.merge(sut.getUnknownType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(), Set.of(c1, c4), null))),
+                                () -> assertThat(a4Result.merge(sut.getUnknownType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(), Set.of(c3), null)))
+                );
+        }
+
+        @Test
+        void consistentErrorTest() {
+                var c1Result = tester.getPreservedType(c1);
+                var a4Result = tester.getPreservedType(a4);
+                var expected = new InferredType(Set.of(c1, a1, a4), Set.of(), null);
+                assertAll(
+                                () -> assertThat(c1Result.merge(a4Result.asInferredType(), TruthValue.ERROR), is(expected)),
+                                () -> assertThat(a4Result.merge(c1Result.asInferredType(), TruthValue.ERROR), is(expected))
+                );
+        }
+
+        @Test
+        void consistentUnknownTest() {
+                var c1Result = tester.getPreservedType(c1);
+                var a4Result = tester.getPreservedType(a4);
+                assertAll(
+                                () -> assertThat(c1Result.merge(a4Result.asInferredType(), TruthValue.UNKNOWN),
+                                                is(a4Result.asInferredType())),
+                                () -> assertThat(a4Result.merge(c1Result.asInferredType(), TruthValue.UNKNOWN),
+                                                is(c1Result.asInferredType()))
+                );
+        }
+
+        @Test
+        void inconsistentMustTest() {
+                var a1Result = tester.getPreservedType(a1);
+                var c3Result = tester.getPreservedType(c3);
+                assertAll(
+                                () -> assertThat(a1Result.merge(c3Result.asInferredType(), TruthValue.TRUE),
+                                                is(new InferredType(Set.of(a1, a3, c3), Set.of(), null))),
+                                () -> assertThat(c3Result.merge(a1Result.asInferredType(), TruthValue.TRUE),
+                                                is(new InferredType(Set.of(a1, a3, a4, c3), Set.of(), null)))
+                );
+        }
+
+        @Test
+        void inconsistentMayNotTest() {
+                var a1Result = tester.getPreservedType(a1);
+                var a4Result = tester.getPreservedType(a4);
+                var c1Result = tester.getPreservedType(c1);
+                assertAll(
+                                () -> assertThat(a4Result.merge(a1Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a1, a4), Set.of(), null))),
+                                () -> assertThat(a1Result.merge(c1Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a1, a4, c1), Set.of(), null))),
+                                () -> assertThat(a4Result.merge(c1Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a1, a4, c1), Set.of(), null))),
+                                () -> assertThat(a1Result.merge(a1Result.asInferredType(), TruthValue.FALSE),
+                                                is(new InferredType(Set.of(a1, a4), Set.of(), null)))
+                );
+        }
+
+        @Test
+        void vacuousMustTest() {
+                var c1Result = tester.getPreservedType(c1);
+                var a5Result = tester.getPreservedType(a5);
+                assertAll(
+                                () -> assertThat(c1Result.merge(a5Result.asInferredType(), TruthValue.TRUE),
+                                                is(new InferredType(Set.of(a1, a4, a5, c1), Set.of(), null))),
+                                () -> assertThat(a5Result.merge(c1Result.asInferredType(), TruthValue.TRUE),
+                                                is(new InferredType(Set.of(a1, a4, a5, c1), Set.of(), null)))
+                );
+        }
+
+        @Test
+        void vacuousMayNotTest() {
+                var c1Result = tester.getPreservedType(c1);
+                var a5Result = tester.getPreservedType(a5);
+                assertAll(
+                                () -> assertThat(c1Result.merge(a5Result.asInferredType(), TruthValue.FALSE),
+                                                is(a5Result.asInferredType())),
+                                () -> assertThat(a5Result.merge(c1Result.asInferredType(), TruthValue.FALSE),
+                                                is(c1Result.asInferredType()))
+                );
+        }
+
+        @Test
+        void vacuousErrorTest() {
+                var c1Result = tester.getPreservedType(c1);
+                var a5Result = tester.getPreservedType(a5);
+                assertAll(
+                                () -> assertThat(c1Result.merge(a5Result.asInferredType(), TruthValue.ERROR),
+                                                is(new InferredType(Set.of(a1, a4, a5, c1), Set.of(), null))),
+                                () -> assertThat(a5Result.merge(c1Result.asInferredType(), TruthValue.ERROR),
+                                                is(new InferredType(Set.of(a1, a4, a5, c1), Set.of(), null))),
+                                () -> assertThat(a5Result.merge(a5Result.asInferredType(), TruthValue.ERROR),
+                                                is(a5Result.asInferredType()))
+                );
+        }
+}
diff --git a/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTest.java b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTest.java
new file mode 100644
index 00000000..d0ef9d57
--- /dev/null
+++ b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTest.java
@@ -0,0 +1,205 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import org.junit.jupiter.api.Test;
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.representation.TruthValue;
+
+import java.util.LinkedHashMap;
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static org.junit.jupiter.api.Assertions.assertAll;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+class TypeAnalyzerTest {
+        @Test
+        void directSupertypesTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var c3 = new PartialRelation("C3", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertypes(c2, c3).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(c3).build());
+                typeInfoMap.put(c3, TypeInfo.builder().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+
+                assertAll(
+                                () -> tester.assertConcreteType(c1),
+                                () -> tester.assertConcreteType(c2, c1),
+                                () -> tester.assertConcreteType(c3, c2)
+                );
+        }
+
+        @Test
+        void typeEliminationAbstractToConcreteTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var a11 = new PartialRelation("A11", 1);
+                var a12 = new PartialRelation("A12", 1);
+                var a21 = new PartialRelation("A21", 1);
+                var a22 = new PartialRelation("A22", 1);
+                var a3 = new PartialRelation("A3", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(a3, TypeInfo.builder().abstractType().build());
+                typeInfoMap.put(a21, TypeInfo.builder().abstractType().supertype(a3).build());
+                typeInfoMap.put(a22, TypeInfo.builder().abstractType().supertype(a3).build());
+                typeInfoMap.put(a11, TypeInfo.builder().abstractType().supertypes(a21, a22).build());
+                typeInfoMap.put(a12, TypeInfo.builder().abstractType().supertypes(a21, a22).build());
+                typeInfoMap.put(c1, TypeInfo.builder().supertypes(a11, a12).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(a3).build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+
+                assertAll(
+                                () -> tester.assertConcreteType(c1),
+                                () -> tester.assertConcreteType(c2),
+                                () -> tester.assertEliminatedType(a11, c1),
+                                () -> tester.assertEliminatedType(a12, c1),
+                                () -> tester.assertEliminatedType(a21, c1),
+                                () -> tester.assertEliminatedType(a22, c1),
+                                () -> tester.assertAbstractType(a3, c1, c2)
+                );
+        }
+
+        @Test
+        void typeEliminationConcreteToAbstractTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var a11 = new PartialRelation("A11", 1);
+                var a12 = new PartialRelation("A12", 1);
+                var a21 = new PartialRelation("A21", 1);
+                var a22 = new PartialRelation("A22", 1);
+                var a3 = new PartialRelation("A3", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertypes(a11, a12).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(a3).build());
+                typeInfoMap.put(a11, TypeInfo.builder().abstractType().supertypes(a21, a22).build());
+                typeInfoMap.put(a12, TypeInfo.builder().abstractType().supertypes(a21, a22).build());
+                typeInfoMap.put(a21, TypeInfo.builder().abstractType().supertype(a3).build());
+                typeInfoMap.put(a22, TypeInfo.builder().abstractType().supertype(a3).build());
+                typeInfoMap.put(a3, TypeInfo.builder().abstractType().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+
+                assertAll(
+                                () -> tester.assertConcreteType(c1),
+                                () -> tester.assertConcreteType(c2),
+                                () -> tester.assertEliminatedType(a11, c1),
+                                () -> tester.assertEliminatedType(a12, c1),
+                                () -> tester.assertEliminatedType(a21, c1),
+                                () -> tester.assertEliminatedType(a22, c1),
+                                () -> tester.assertAbstractType(a3, c1, c2)
+                );
+        }
+
+        @Test
+        void preserveConcreteTypeTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var a1 = new PartialRelation("A1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var a2 = new PartialRelation("A2", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(a1, TypeInfo.builder().abstractType().supertype(c2).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(a2).build());
+                typeInfoMap.put(a2, TypeInfo.builder().abstractType().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+
+                assertAll(
+                                () -> tester.assertConcreteType(c1),
+                                () -> tester.assertEliminatedType(a1, c1),
+                                () -> tester.assertConcreteType(c2, c1),
+                                () -> tester.assertEliminatedType(a2, c2)
+                );
+        }
+
+        @Test
+        void mostGeneralCurrentTypeTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var c3 = new PartialRelation("C3", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertype(c3).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(c3).build());
+                typeInfoMap.put(c3, TypeInfo.builder().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+                var c3Result = tester.getPreservedType(c3);
+
+                var expected = new InferredType(Set.of(c3), Set.of(c1, c2, c3), c3);
+                assertAll(
+                                () -> assertThat(tester.getInferredType(c3), is(expected)),
+                                () -> assertThat(c3Result.merge(sut.getUnknownType(), TruthValue.TRUE), is(expected))
+                );
+        }
+
+        @Test
+        void preferFirstConcreteTypeTest() {
+                var a1 = new PartialRelation("A1", 1);
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var c3 = new PartialRelation("C3", 1);
+                var c4 = new PartialRelation("C4", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(c3, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(c4, TypeInfo.builder().supertype(c3).build());
+                typeInfoMap.put(a1, TypeInfo.builder().abstractType().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+                var c1Result = tester.getPreservedType(c1);
+                var a1Result = tester.getPreservedType(a1);
+
+                assertThat(c1Result.merge(a1Result.asInferredType(), TruthValue.FALSE),
+                                is(new InferredType(Set.of(a1), Set.of(c2, c3, c4), c2)));
+        }
+
+        @Test
+        void preferFirstMostGeneralConcreteTypeTest() {
+                var a1 = new PartialRelation("A1", 1);
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var c3 = new PartialRelation("C3", 1);
+                var c4 = new PartialRelation("C4", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c4, TypeInfo.builder().supertype(c3).build());
+                typeInfoMap.put(c3, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(c1, TypeInfo.builder().supertype(a1).build());
+                typeInfoMap.put(a1, TypeInfo.builder().abstractType().build());
+
+                var sut = new TypeAnalyzer(typeInfoMap);
+                var tester = new TypeAnalyzerTester(sut);
+                var c1Result = tester.getPreservedType(c1);
+                var a1Result = tester.getPreservedType(a1);
+
+                assertThat(c1Result.merge(a1Result.asInferredType(), TruthValue.FALSE),
+                                is(new InferredType(Set.of(a1), Set.of(c2, c3, c4), c3)));
+        }
+
+        @Test
+        void circularTypeHierarchyTest() {
+                var c1 = new PartialRelation("C1", 1);
+                var c2 = new PartialRelation("C2", 1);
+                var typeInfoMap = new LinkedHashMap<PartialRelation, TypeInfo>();
+                typeInfoMap.put(c1, TypeInfo.builder().supertype(c2).build());
+                typeInfoMap.put(c2, TypeInfo.builder().supertype(c1).build());
+
+                assertThrows(IllegalArgumentException.class, () -> new TypeAnalyzer(typeInfoMap));
+        }
+}
diff --git a/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTester.java b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTester.java
new file mode 100644
index 00000000..2924816e
--- /dev/null
+++ b/subprojects/store-reasoning/src/test/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeAnalyzerTester.java
@@ -0,0 +1,56 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.typehierarchy;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.is;
+
+class TypeAnalyzerTester {
+        private final TypeAnalyzer sut;
+
+        public TypeAnalyzerTester(TypeAnalyzer sut) {
+                this.sut = sut;
+        }
+
+        public void assertAbstractType(PartialRelation partialRelation, PartialRelation... directSubtypes) {
+                assertPreservedType(partialRelation, true, false, directSubtypes);
+        }
+
+        public void assertVacuousType(PartialRelation partialRelation) {
+                assertPreservedType(partialRelation, true, true);
+        }
+
+        public void assertConcreteType(PartialRelation partialRelation, PartialRelation... directSubtypes) {
+                assertPreservedType(partialRelation, false, false, directSubtypes);
+        }
+
+        private void assertPreservedType(PartialRelation partialRelation, boolean isAbstract, boolean isVacuous,
+                                                                         PartialRelation... directSubtypes) {
+                var result = sut.getAnalysisResults().get(partialRelation);
+                assertThat(result, is(instanceOf(PreservedType.class)));
+                var preservedResult = (PreservedType) result;
+                assertThat(preservedResult.isAbstractType(), is(isAbstract));
+                assertThat(preservedResult.isVacuous(), is(isVacuous));
+                assertThat(preservedResult.getDirectSubtypes(), hasItems(directSubtypes));
+        }
+
+        public void assertEliminatedType(PartialRelation partialRelation, PartialRelation replacement) {
+                var result = sut.getAnalysisResults().get(partialRelation);
+                assertThat(result, is(instanceOf(EliminatedType.class)));
+                assertThat(((EliminatedType) result).replacement(), is(replacement));
+        }
+
+        public PreservedType getPreservedType(PartialRelation partialRelation) {
+                return (PreservedType) sut.getAnalysisResults().get(partialRelation);
+        }
+
+        public InferredType getInferredType(PartialRelation partialRelation) {
+                return getPreservedType(partialRelation).asInferredType();
+        }
+}
diff --git a/subprojects/store/build.gradle b/subprojects/store/build.gradle
deleted file mode 100644
index 370d094b..00000000
--- a/subprojects/store/build.gradle
+++ /dev/null
@@ -1,4 +0,0 @@
-plugins {
-        id 'refinery-java-library'
-        id 'refinery-jmh'
-}
diff --git a/subprojects/store/build.gradle.kts b/subprojects/store/build.gradle.kts
new file mode 100644
index 00000000..2c485020
--- /dev/null
+++ b/subprojects/store/build.gradle.kts
@@ -0,0 +1,10 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+
+plugins {
+        id("tools.refinery.gradle.java-library")
+        id("tools.refinery.gradle.jmh")
+}
diff --git a/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutBenchmark.java b/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutBenchmark.java
index cdf3d3c8..485fda3d 100644
--- a/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutBenchmark.java
+++ b/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutBenchmark.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.benchmarks;
 
 import java.util.ArrayList;
diff --git a/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutExecutionPlan.java b/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutExecutionPlan.java
index 5484f115..7e89cd06 100644
--- a/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutExecutionPlan.java
+++ b/subprojects/store/src/jmh/java/tools/refinery/store/map/benchmarks/ImmutablePutExecutionPlan.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.benchmarks;
 
 import java.util.Random;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/AbstractModelAdapterBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/AbstractModelAdapterBuilder.java
index 4c142217..8d3e998e 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/AbstractModelAdapterBuilder.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/adapter/AbstractModelAdapterBuilder.java
@@ -1,27 +1,48 @@
 package tools.refinery.store.adapter;
-
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
 
-public abstract class AbstractModelAdapterBuilder implements ModelAdapterBuilder {
-        private final ModelStoreBuilder storeBuilder;
+public abstract class AbstractModelAdapterBuilder<T extends ModelStoreAdapter> implements ModelAdapterBuilder {
+        private boolean configured;
 
-        protected AbstractModelAdapterBuilder(ModelStoreBuilder storeBuilder) {
-                this.storeBuilder = storeBuilder;
+        @Override
+        public boolean isConfigured() {
+                return configured;
         }
 
-        @Override
-        public <T extends ModelAdapterBuilder> T with(ModelAdapterBuilderFactory<?, ?, T> adapterBuilderFactory) {
-                return storeBuilder.with(adapterBuilderFactory);
+        protected void checkConfigured() {
+                if (!configured) {
+                        throw new IllegalStateException("Model adapter builder was not configured");
+                }
+        }
+
+        protected void checkNotConfigured() {
+                if (configured) {
+                        throw new IllegalStateException("Model adapter builder was already configured");
+                }
+        }
+
+        protected void doConfigure(ModelStoreBuilder storeBuilder) {
+                // Nothing to configure by default.
         }
 
         @Override
-        public ModelStoreBuilder getStoreBuilder() {
-                return storeBuilder;
+        public final void configure(ModelStoreBuilder storeBuilder) {
+                checkNotConfigured();
+                doConfigure(storeBuilder);
+                configured = true;
         }
 
+        protected abstract T doBuild(ModelStore store);
+
         @Override
-        public ModelStore build() {
-                return storeBuilder.build();
+        public final T build(ModelStore store) {
+                checkConfigured();
+                return doBuild(store);
         }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterList.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterList.java
deleted file mode 100644
index 74bae6f0..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterList.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package tools.refinery.store.adapter;
-
-import org.jetbrains.annotations.NotNull;
-
-import java.util.*;
-import java.util.function.Consumer;
-
-public class AdapterList<T> implements Iterable<T> {
-        private final List<AnyModelAdapterType> adapterTypes;
-        private final List<T> adapters;
-
-        public AdapterList() {
-                adapterTypes = new ArrayList<>();
-                adapters = new ArrayList<>();
-        }
-
-        public AdapterList(int adapterCount) {
-                adapterTypes = new ArrayList<>(adapterCount);
-                adapters = new ArrayList<>(adapterCount);
-        }
-
-        public int size() {
-                return adapters.size();
-        }
-
-        public void add(AnyModelAdapterType adapterType, T adapter) {
-                adapterTypes.add(adapterType);
-                adapters.add(adapter);
-        }
-
-        public <U extends T> Optional<U> tryGet(AnyModelAdapterType adapterType, Class<? extends U> adapterClass) {
-                int size = size();
-                for (int i = 0; i < size; i++) {
-                        if (getType(i).supports(adapterType)) {
-                                return Optional.of(adapterClass.cast(get(i)));
-                        }
-                }
-                return Optional.empty();
-        }
-
-        public <U extends T> U get(AnyModelAdapterType adapterType, Class<U> adapterClass) {
-                return tryGet(adapterType, adapterClass).orElseThrow(() -> new IllegalArgumentException(
-                                "No %s was configured".formatted(adapterType)));
-        }
-
-        public AnyModelAdapterType getType(int i) {
-                return adapterTypes.get(i);
-        }
-
-        public T get(int i) {
-                return adapters.get(i);
-        }
-
-        public Collection<AnyModelAdapterType> getAdapterTypes() {
-                return Collections.unmodifiableCollection(adapterTypes);
-        }
-
-        public Iterable<Entry<T>> withAdapterTypes() {
-                return () -> new Iterator<>() {
-                        private int i = 0;
-
-                        @Override
-                        public boolean hasNext() {
-                                return i < size();
-                        }
-
-                        @Override
-                        public Entry<T> next() {
-                                if (i >= size()) {
-                                        throw new NoSuchElementException();
-                                }
-                                var entry = new Entry<>(getType(i), get(i));
-                                i++;
-                                return entry;
-                        }
-                };
-        }
-
-        @NotNull
-        @Override
-        public Iterator<T> iterator() {
-                return adapters.iterator();
-        }
-
-        @Override
-        public void forEach(Consumer<? super T> action) {
-                adapters.forEach(action);
-        }
-
-        @Override
-        public Spliterator<T> spliterator() {
-                return adapters.spliterator();
-        }
-
-        public record Entry<T>(AnyModelAdapterType adapterType, T adapter) {
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterUtils.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterUtils.java
new file mode 100644
index 00000000..556e99f0
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/adapter/AdapterUtils.java
@@ -0,0 +1,33 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.adapter;
+
+import java.util.Collection;
+import java.util.Optional;
+
+public class AdapterUtils {
+        private AdapterUtils() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static <T, U extends T> Optional<U> tryGetAdapter(Collection<T> adapters, Class<? extends U> type) {
+                var iterator = adapters.stream().filter(type::isInstance).iterator();
+                if (!iterator.hasNext()) {
+                        return Optional.empty();
+                }
+                var adapter = type.cast(iterator.next());
+                if (iterator.hasNext()) {
+                        throw new IllegalArgumentException("Ambiguous adapter: both %s and %s match %s"
+                                        .formatted(adapter.getClass().getName(), iterator.next().getClass().getName(), type.getName()));
+                }
+                return Optional.of(adapter);
+        }
+
+        public static <T> T getAdapter(Collection<? super T> adapters, Class<T> type) {
+                return tryGetAdapter(adapters, type).orElseThrow(() -> new IllegalArgumentException(
+                                "No %s adapter was configured".formatted(type.getName())));
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/AnyModelAdapterType.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/AnyModelAdapterType.java
deleted file mode 100644
index 37a247fe..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/AnyModelAdapterType.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package tools.refinery.store.adapter;
-
-import java.util.Collection;
-
-public sealed interface AnyModelAdapterType permits ModelAdapterType {
-        Class<? extends ModelAdapter> getModelAdapterClass();
-
-        Class<? extends ModelStoreAdapter> getModelStoreAdapterClass();
-
-        Class<? extends ModelAdapterBuilder> getModelAdapterBuilderClass();
-
-        Collection<AnyModelAdapterType> getSupportedAdapterTypes();
-
-        default boolean supports(AnyModelAdapterType targetAdapter) {
-                return getSupportedAdapterTypes().contains(targetAdapter);
-        }
-
-        String getName();
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapter.java
index aa079e01..672007aa 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapter.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.adapter;
 
 import tools.refinery.store.model.Model;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilder.java
index 64b3e59f..75e5e07d 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilder.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilder.java
@@ -1,17 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.adapter;
 
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
 
 public interface ModelAdapterBuilder {
-        ModelStoreAdapter createStoreAdapter(ModelStore store);
+        boolean isConfigured();
 
-        <T extends ModelAdapterBuilder> T with(ModelAdapterBuilderFactory<?, ?, T> adapterBuilderFactory);
+        void configure(ModelStoreBuilder storeBuilder);
 
-        ModelStoreBuilder getStoreBuilder();
-
-        default void configure() {
-        }
-
-        ModelStore build();
+        ModelStoreAdapter build(ModelStore store);
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilderFactory.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilderFactory.java
deleted file mode 100644
index 7c9b01bc..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterBuilderFactory.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package tools.refinery.store.adapter;
-
-import tools.refinery.store.model.ModelStoreBuilder;
-
-public abstract class ModelAdapterBuilderFactory<T1 extends ModelAdapter, T2 extends ModelStoreAdapter,
-                T3 extends ModelAdapterBuilder> extends ModelAdapterType<T1, T2, T3> {
-
-        protected ModelAdapterBuilderFactory(Class<T1> modelAdapterClass, Class<T2> modelStoreAdapterClass,
-                                                                                 Class<T3> modelAdapterBuilderClass) {
-                super(modelAdapterClass, modelStoreAdapterClass, modelAdapterBuilderClass);
-        }
-
-        public abstract T3 createBuilder(ModelStoreBuilder storeBuilder);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterType.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterType.java
deleted file mode 100644
index 82ddeb12..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelAdapterType.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package tools.refinery.store.adapter;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.model.ModelStore;
-
-import java.lang.reflect.Method;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-
-public abstract non-sealed class ModelAdapterType<T1 extends ModelAdapter, T2 extends ModelStoreAdapter,
-                T3 extends ModelAdapterBuilder> implements AnyModelAdapterType {
-        private final Class<? extends T1> modelAdapterClass;
-        private final Class<? extends T2> modelStoreAdapterClass;
-        private final Class<? extends T3> modelAdapterBuilderClass;
-        private final Set<AnyModelAdapterType> supportedAdapters = new HashSet<>();
-
-        protected ModelAdapterType(Class<T1> modelAdapterClass, Class<T2> modelStoreAdapterClass,
-                                                           Class<T3> modelAdapterBuilderClass) {
-                checkReturnType(modelAdapterClass, modelStoreAdapterClass, "createModelAdapter", Model.class);
-                checkReturnType(modelStoreAdapterClass, modelAdapterBuilderClass, "createStoreAdapter", ModelStore.class);
-                this.modelAdapterClass = modelAdapterClass;
-                this.modelStoreAdapterClass = modelStoreAdapterClass;
-                this.modelAdapterBuilderClass = modelAdapterBuilderClass;
-                supportedAdapters.add(this);
-        }
-
-        private void checkReturnType(Class<?> expectedReturnType, Class<?> ownerClass, String methodName,
-                                                                 Class<?>... argumentTypes) {
-                Method method;
-                try {
-                        method = ownerClass.getMethod(methodName, argumentTypes);
-                } catch (NoSuchMethodException e) {
-                        throw new IllegalStateException("Invalid %s: %s#%s method is required"
-                                        .formatted(this, ownerClass.getName(), methodName), e);
-                }
-                var returnType = method.getReturnType();
-                if (!expectedReturnType.isAssignableFrom(returnType)) {
-                        throw new IllegalStateException("Invalid %s: %s is not assignable from the return type %s of %s#%s"
-                                        .formatted(this, expectedReturnType.getName(), returnType.getCanonicalName(),
-                                                        ownerClass.getName(), methodName));
-                }
-        }
-
-        protected void extendsAdapter(ModelAdapterType<? super T1, ? super T2, ? super T3> superAdapter) {
-                supportedAdapters.addAll(superAdapter.supportedAdapters);
-        }
-
-        @Override
-        public final Class<? extends T1> getModelAdapterClass() {
-                return modelAdapterClass;
-        }
-
-        @Override
-        public final Class<? extends T2> getModelStoreAdapterClass() {
-                return modelStoreAdapterClass;
-        }
-
-        @Override
-        public final Class<? extends T3> getModelAdapterBuilderClass() {
-                return modelAdapterBuilderClass;
-        }
-
-        @Override
-        public Collection<AnyModelAdapterType> getSupportedAdapterTypes() {
-                return Collections.unmodifiableCollection(supportedAdapters);
-        }
-
-        @Override
-        public String getName() {
-                return "%s.ADAPTER".formatted(this.getClass().getName());
-        }
-
-        @Override
-        public String toString() {
-                return getName();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelStoreAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelStoreAdapter.java
index 1eb40ada..bc5f7b6b 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelStoreAdapter.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/adapter/ModelStoreAdapter.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.adapter;
 
 import tools.refinery.store.model.Model;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/AnyVersionedMap.java b/subprojects/store/src/main/java/tools/refinery/store/map/AnyVersionedMap.java
index ead79878..01099eb0 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/AnyVersionedMap.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/AnyVersionedMap.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public sealed interface AnyVersionedMap extends Versioned permits VersionedMap {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/ContentHashCode.java b/subprojects/store/src/main/java/tools/refinery/store/map/ContentHashCode.java
index 8deeab23..cbea05e1 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/ContentHashCode.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/ContentHashCode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public enum ContentHashCode {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/ContinousHashProvider.java b/subprojects/store/src/main/java/tools/refinery/store/map/ContinousHashProvider.java
index 75f1e2ab..8e451230 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/ContinousHashProvider.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/ContinousHashProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import tools.refinery.store.map.internal.Node;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/Cursor.java b/subprojects/store/src/main/java/tools/refinery/store/map/Cursor.java
index b420585c..3bdca104 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/Cursor.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/Cursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import java.util.Set;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/CursorAsIterator.java b/subprojects/store/src/main/java/tools/refinery/store/map/CursorAsIterator.java
index 65ae6648..c7e4d279 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/CursorAsIterator.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/CursorAsIterator.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import java.util.Iterator;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/Cursors.java b/subprojects/store/src/main/java/tools/refinery/store/map/Cursors.java
new file mode 100644
index 00000000..0a94d449
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/Cursors.java
@@ -0,0 +1,41 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.map;
+
+public final class Cursors {
+    private Cursors() {
+        throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+    }
+
+    public static <K, V> Cursor<K, V> empty() {
+        return new Empty<>();
+    }
+
+    private static class Empty<K, V> implements Cursor<K, V> {
+        private boolean terminated = false;
+
+        @Override
+        public K getKey() {
+            return null;
+        }
+
+        @Override
+        public V getValue() {
+            return null;
+        }
+
+        @Override
+        public boolean isTerminated() {
+            return terminated;
+        }
+
+        @Override
+        public boolean move() {
+            terminated = true;
+            return false;
+        }
+    }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/DiffCursor.java b/subprojects/store/src/main/java/tools/refinery/store/map/DiffCursor.java
index 701f3ec8..4322e041 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/DiffCursor.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/DiffCursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public interface DiffCursor<K, V> extends Cursor<K,V> {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/MapAsIterable.java b/subprojects/store/src/main/java/tools/refinery/store/map/MapAsIterable.java
index 6b986732..199b548f 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/MapAsIterable.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/MapAsIterable.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import java.util.Iterator;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/Versioned.java b/subprojects/store/src/main/java/tools/refinery/store/map/Versioned.java
index 6a23e9d5..55720db3 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/Versioned.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/Versioned.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public interface Versioned {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMap.java b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMap.java
index 08ce1dbd..c8226c3e 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMap.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMap.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public non-sealed interface VersionedMap<K, V> extends AnyVersionedMap {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStore.java b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStore.java
index 7768287a..b24c404c 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStore.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStore.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import tools.refinery.store.map.internal.VersionedMapStoreFactoryBuilderImpl;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreConfiguration.java b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreConfiguration.java
index 3856460d..b00cd961 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreConfiguration.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreConfiguration.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 public class VersionedMapStoreConfiguration {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreImpl.java b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreImpl.java
index beeed110..a934d59e 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/VersionedMapStoreImpl.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map;
 
 import tools.refinery.store.map.internal.*;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/HashClash.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/HashClash.java
index 0806c486..a357fbce 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/HashClash.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/HashClash.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 enum HashClash {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/ImmutableNode.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/ImmutableNode.java
index 92446711..d052318f 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/ImmutableNode.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/ImmutableNode.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 import java.util.Arrays;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapCursor.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapCursor.java
index 7e4f82e8..d42519b2 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapCursor.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapCursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 import tools.refinery.store.map.AnyVersionedMap;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapDiffCursor.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapDiffCursor.java
index 59e8d738..fb1d5d2b 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapDiffCursor.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MapDiffCursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 import tools.refinery.store.map.AnyVersionedMap;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MutableNode.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MutableNode.java
index 81bf6188..bb85deb9 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/MutableNode.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/MutableNode.java
@@ -1,10 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
+import tools.refinery.store.map.ContinousHashProvider;
+
 import java.util.Arrays;
 import java.util.Map;
 
-import tools.refinery.store.map.ContinousHashProvider;
-
 public class MutableNode<K, V> extends Node<K, V> {
         int cachedHash;
         protected boolean cachedHashValid;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/Node.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/Node.java
index 3dd332da..4b44f760 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/Node.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/Node.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 import java.util.Map;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/OldValueBox.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/OldValueBox.java
index 5534c703..354af51d 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/OldValueBox.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/OldValueBox.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 public class OldValueBox<V>{
diff --git a/subprojects/store/src/main/java/tools/refinery/store/map/internal/VersionedMapImpl.java b/subprojects/store/src/main/java/tools/refinery/store/map/internal/VersionedMapImpl.java
index 2ceca463..c107f7e0 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/map/internal/VersionedMapImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/map/internal/VersionedMapImpl.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.internal;
 
 import tools.refinery.store.map.*;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/AnyInterpretation.java b/subprojects/store/src/main/java/tools/refinery/store/model/AnyInterpretation.java
index d18ba71d..f906b48a 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/AnyInterpretation.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/AnyInterpretation.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.representation.AnySymbol;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/Interpretation.java b/subprojects/store/src/main/java/tools/refinery/store/model/Interpretation.java
index 55949d0c..26ad9a69 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/Interpretation.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/Interpretation.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.map.Cursor;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/InterpretationListener.java b/subprojects/store/src/main/java/tools/refinery/store/model/InterpretationListener.java
index 73950779..6f7b24c1 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/InterpretationListener.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/InterpretationListener.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.tuple.Tuple;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/Model.java b/subprojects/store/src/main/java/tools/refinery/store/model/Model.java
index 6ca1ac7b..d58d91c3 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/Model.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/Model.java
@@ -1,7 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.adapter.ModelAdapter;
-import tools.refinery.store.adapter.ModelAdapterType;
 import tools.refinery.store.map.Versioned;
 import tools.refinery.store.representation.AnySymbol;
 import tools.refinery.store.representation.Symbol;
@@ -25,9 +29,9 @@ public interface Model extends Versioned {
 
         ModelDiffCursor getDiffCursor(long to);
 
-        <T extends ModelAdapter> Optional<T> tryGetAdapter(ModelAdapterType<? extends T, ?, ?> adapterType);
+        <T extends ModelAdapter> Optional<T> tryGetAdapter(Class<? extends T> adapterType);
 
-        <T extends ModelAdapter> T getAdapter(ModelAdapterType<T, ?, ?> adapterType);
+        <T extends ModelAdapter> T getAdapter(Class<T> adapterType);
 
         void addListener(ModelListener listener);
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/ModelDiffCursor.java b/subprojects/store/src/main/java/tools/refinery/store/model/ModelDiffCursor.java
index 97bf2039..7b236891 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/ModelDiffCursor.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/ModelDiffCursor.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.map.DiffCursor;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/ModelListener.java b/subprojects/store/src/main/java/tools/refinery/store/model/ModelListener.java
index f67540bb..a9ad8cfd 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/ModelListener.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/ModelListener.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 public interface ModelListener {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/ModelStore.java b/subprojects/store/src/main/java/tools/refinery/store/model/ModelStore.java
index 2e7e62c3..b10eb8a4 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/ModelStore.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/ModelStore.java
@@ -1,6 +1,10 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
-import tools.refinery.store.adapter.ModelAdapterType;
 import tools.refinery.store.adapter.ModelStoreAdapter;
 import tools.refinery.store.model.internal.ModelStoreBuilderImpl;
 import tools.refinery.store.representation.AnySymbol;
@@ -20,9 +24,9 @@ public interface ModelStore {
 
         ModelDiffCursor getDiffCursor(long from, long to);
 
-        <T extends ModelStoreAdapter> Optional<T> tryGetAdapter(ModelAdapterType<?, ? extends T, ?> adapterType);
+        <T extends ModelStoreAdapter> Optional<T> tryGetAdapter(Class<? extends T> adapterType);
 
-        <T extends ModelStoreAdapter> T getAdapter(ModelAdapterType<?, T, ?> adapterType);
+        <T extends ModelStoreAdapter> T getAdapter(Class<T> adapterType);
 
         static ModelStoreBuilder builder() {
                 return new ModelStoreBuilderImpl();
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/ModelStoreBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/model/ModelStoreBuilder.java
index 289099da..3a4024b5 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/ModelStoreBuilder.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/ModelStoreBuilder.java
@@ -1,8 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.adapter.ModelAdapterBuilder;
-import tools.refinery.store.adapter.ModelAdapterBuilderFactory;
-import tools.refinery.store.adapter.ModelAdapterType;
 import tools.refinery.store.representation.AnySymbol;
 import tools.refinery.store.representation.Symbol;
 
@@ -26,11 +29,11 @@ public interface ModelStoreBuilder {
 
         <T> ModelStoreBuilder symbol(Symbol<T> symbol);
 
-        <T extends ModelAdapterBuilder> T with(ModelAdapterBuilderFactory<?, ?, T> adapterBuilderFactory);
+        <T extends ModelAdapterBuilder> ModelStoreBuilder with(T adapterBuilder);
 
-        <T extends ModelAdapterBuilder> Optional<T> tryGetAdapter(ModelAdapterType<?, ?, ? extends T> adapterType);
+        <T extends ModelAdapterBuilder> Optional<T> tryGetAdapter(Class<? extends T> adapterType);
 
-        <T extends ModelAdapterBuilder> T getAdapter(ModelAdapterType<?, ?, T> adapterType);
+        <T extends ModelAdapterBuilder> T getAdapter(Class<T> adapterType);
 
         ModelStore build();
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProvider.java b/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProvider.java
index 1183b8f2..fdd4425e 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProvider.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProvider.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.map.ContinousHashProvider;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProviderBitMagic.java b/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProviderBitMagic.java
index 33059a1b..14116a90 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProviderBitMagic.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/TupleHashProviderBitMagic.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model;
 
 import tools.refinery.store.map.ContinousHashProvider;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelAction.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelAction.java
index f68859db..dbd95d80 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelAction.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelAction.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
 public enum ModelAction {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelImpl.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelImpl.java
index 9eb438c4..c5475a1a 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelImpl.java
@@ -1,9 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
-import tools.refinery.store.adapter.AdapterList;
-import tools.refinery.store.adapter.AnyModelAdapterType;
+import tools.refinery.store.adapter.AdapterUtils;
 import tools.refinery.store.adapter.ModelAdapter;
-import tools.refinery.store.adapter.ModelAdapterType;
 import tools.refinery.store.map.DiffCursor;
 import tools.refinery.store.model.*;
 import tools.refinery.store.representation.AnySymbol;
@@ -16,7 +19,7 @@ public class ModelImpl implements Model {
         private final ModelStore store;
         private long state;
         private Map<? extends AnySymbol, ? extends VersionedInterpretation<?>> interpretations;
-        private final AdapterList<ModelAdapter> adapters;
+        private final List<ModelAdapter> adapters;
         private final List<ModelListener> listeners = new ArrayList<>();
         private boolean uncommittedChanges;
         private ModelAction pendingAction = ModelAction.NONE;
@@ -25,7 +28,7 @@ public class ModelImpl implements Model {
         ModelImpl(ModelStore store, long state, int adapterCount) {
                 this.store = store;
                 this.state = state;
-                adapters = new AdapterList<>(adapterCount);
+                adapters = new ArrayList<>(adapterCount);
         }
 
         void setInterpretations(Map<? extends AnySymbol, ? extends VersionedInterpretation<?>> interpretations) {
@@ -162,17 +165,17 @@ public class ModelImpl implements Model {
         }
 
         @Override
-        public <T extends ModelAdapter> Optional<T> tryGetAdapter(ModelAdapterType<? extends T, ?, ?> adapterType) {
-                return adapters.tryGet(adapterType, adapterType.getModelAdapterClass());
+        public <T extends ModelAdapter> Optional<T> tryGetAdapter(Class<? extends T> adapterType) {
+                return AdapterUtils.tryGetAdapter(adapters, adapterType);
         }
 
         @Override
-        public <T extends ModelAdapter> T getAdapter(ModelAdapterType<T, ?, ?> adapterType) {
-                return adapters.get(adapterType, adapterType.getModelAdapterClass());
+        public <T extends ModelAdapter> T getAdapter(Class<T> adapterType) {
+                return AdapterUtils.getAdapter(adapters, adapterType);
         }
 
-        void addAdapter(AnyModelAdapterType adapterType, ModelAdapter adapter) {
-                adapters.add(adapterType, adapter);
+        void addAdapter(ModelAdapter adapter) {
+                adapters.add(adapter);
         }
 
         @Override
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreBuilderImpl.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreBuilderImpl.java
index 79f7195d..aafbe130 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreBuilderImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreBuilderImpl.java
@@ -1,9 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
-import tools.refinery.store.adapter.AdapterList;
+import tools.refinery.store.adapter.AdapterUtils;
 import tools.refinery.store.adapter.ModelAdapterBuilder;
-import tools.refinery.store.adapter.ModelAdapterBuilderFactory;
-import tools.refinery.store.adapter.ModelAdapterType;
 import tools.refinery.store.map.VersionedMapStore;
 import tools.refinery.store.map.VersionedMapStoreImpl;
 import tools.refinery.store.model.ModelStore;
@@ -18,7 +21,7 @@ import java.util.*;
 public class ModelStoreBuilderImpl implements ModelStoreBuilder {
         private final Set<AnySymbol> allSymbols = new HashSet<>();
         private final Map<SymbolEquivalenceClass<?>, List<AnySymbol>> equivalenceClasses = new HashMap<>();
-        private final AdapterList<ModelAdapterBuilder> adapters = new AdapterList<>();
+        private final List<ModelAdapterBuilder> adapters = new ArrayList<>();
 
         @Override
         public <T> ModelStoreBuilder symbol(Symbol<T> symbol) {
@@ -33,46 +36,25 @@ public class ModelStoreBuilderImpl implements ModelStoreBuilder {
         }
 
         @Override
-        public <T extends ModelAdapterBuilder> T with(ModelAdapterBuilderFactory<?, ?, T> adapterBuilderFactory) {
-                return adapters.<T>tryGet(adapterBuilderFactory, adapterBuilderFactory.getModelAdapterBuilderClass())
-                                .orElseGet(() -> addAdapter(adapterBuilderFactory));
-        }
-
-        private <T extends ModelAdapterBuilder> T addAdapter(ModelAdapterBuilderFactory<?, ?, T> adapterBuilderFactory) {
-                for (var configuredAdapterType : adapters.getAdapterTypes()) {
-                        var intersection = new HashSet<>(adapterBuilderFactory.getSupportedAdapterTypes());
-                        intersection.retainAll(configuredAdapterType.getSupportedAdapterTypes());
-                        if (!intersection.isEmpty()) {
-                                if (configuredAdapterType.supports(adapterBuilderFactory)) {
-                                        // Impossible to end up here from <code>#with</code>, because we should have returned
-                                        // the existing adapter there instead of adding a new one.
-                                        throw new IllegalArgumentException(
-                                                        "Cannot add %s, because it is already provided by configured adapter %s"
-                                                                        .formatted(adapterBuilderFactory, configuredAdapterType));
-                                } else if (adapterBuilderFactory.supports(configuredAdapterType)) {
-                                        throw new IllegalArgumentException(
-                                                        "Cannot add %s, because it provides already configured adapter %s"
-                                                                        .formatted(adapterBuilderFactory, configuredAdapterType));
-                                } else {
-                                        throw new IllegalArgumentException(
-                                                        "Cannot add %s, because configured adapter %s already provides %s"
-                                                                        .formatted(adapterBuilderFactory, configuredAdapterType, intersection));
-                                }
+        public <T extends ModelAdapterBuilder> ModelStoreBuilder with(T adapterBuilder) {
+                for (var existingAdapter : adapters) {
+                        if (existingAdapter.getClass().equals(adapterBuilder.getClass())) {
+                                throw new IllegalArgumentException("%s adapter was already configured for store builder"
+                                                .formatted(adapterBuilder.getClass().getName()));
                         }
                 }
-                var newAdapter = adapterBuilderFactory.createBuilder(this);
-                adapters.add(adapterBuilderFactory, newAdapter);
-                return newAdapter;
+                adapters.add(adapterBuilder);
+                return this;
         }
 
         @Override
-        public <T extends ModelAdapterBuilder> Optional<T> tryGetAdapter(ModelAdapterType<?, ?, ? extends T> adapterType) {
-                return adapters.tryGet(adapterType, adapterType.getModelAdapterBuilderClass());
+        public <T extends ModelAdapterBuilder> Optional<T> tryGetAdapter(Class<? extends T> adapterType) {
+                return AdapterUtils.tryGetAdapter(adapters, adapterType);
         }
 
         @Override
-        public <T extends ModelAdapterBuilder> T getAdapter(ModelAdapterType<?, ?, T> adapterType) {
-                return adapters.get(adapterType, adapterType.getModelAdapterBuilderClass());
+        public <T extends ModelAdapterBuilder> T getAdapter(Class<T> adapterType) {
+                return AdapterUtils.getAdapter(adapters, adapterType);
         }
 
         @Override
@@ -81,13 +63,13 @@ public class ModelStoreBuilderImpl implements ModelStoreBuilder {
                 for (var entry : equivalenceClasses.entrySet()) {
                         createStores(stores, entry.getKey(), entry.getValue());
                 }
-                var modelStore = new ModelStoreImpl(stores, adapters.size());
                 for (int i = adapters.size() - 1; i >= 0; i--) {
-                        adapters.get(i).configure();
+                        adapters.get(i).configure(this);
                 }
-                for (var entry : adapters.withAdapterTypes()) {
-                        var adapter = entry.adapter().createStoreAdapter(modelStore);
-                        modelStore.addAdapter(entry.adapterType(), adapter);
+                var modelStore = new ModelStoreImpl(stores, adapters.size());
+                for (var adapterBuilder : adapters) {
+                        var storeAdapter = adapterBuilder.build(modelStore);
+                        modelStore.addAdapter(storeAdapter);
                 }
                 return modelStore;
         }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreImpl.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreImpl.java
index e8c205e4..60b735e6 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreImpl.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/ModelStoreImpl.java
@@ -1,8 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
-import tools.refinery.store.adapter.AdapterList;
-import tools.refinery.store.adapter.AnyModelAdapterType;
-import tools.refinery.store.adapter.ModelAdapterType;
+import tools.refinery.store.adapter.AdapterUtils;
 import tools.refinery.store.adapter.ModelStoreAdapter;
 import tools.refinery.store.map.DiffCursor;
 import tools.refinery.store.map.VersionedMapStore;
@@ -16,11 +19,11 @@ import java.util.*;
 
 public class ModelStoreImpl implements ModelStore {
         private final Map<? extends AnySymbol, ? extends VersionedMapStore<Tuple, ?>> stores;
-        private final AdapterList<ModelStoreAdapter> adapters;
+        private final List<ModelStoreAdapter> adapters;
 
         ModelStoreImpl(Map<? extends AnySymbol, ? extends VersionedMapStore<Tuple, ?>> stores, int adapterCount) {
                 this.stores = stores;
-                adapters = new AdapterList<>(adapterCount);
+                adapters = new ArrayList<>(adapterCount);
         }
 
         @Override
@@ -59,9 +62,9 @@ public class ModelStoreImpl implements ModelStore {
         }
 
         private void adaptModel(ModelImpl model) {
-                for (var entry : adapters.withAdapterTypes()) {
-                        var adapter = entry.adapter().createModelAdapter(model);
-                        model.addAdapter(entry.adapterType(), adapter);
+                for (var storeAdapter : adapters) {
+                        var adapter = storeAdapter.createModelAdapter(model);
+                        model.addAdapter(adapter);
                 }
         }
 
@@ -86,16 +89,16 @@ public class ModelStoreImpl implements ModelStore {
         }
 
         @Override
-        public <T extends ModelStoreAdapter> Optional<T> tryGetAdapter(ModelAdapterType<?, ? extends T, ?> adapterType) {
-                return adapters.tryGet(adapterType, adapterType.getModelStoreAdapterClass());
+        public <T extends ModelStoreAdapter> Optional<T> tryGetAdapter(Class<? extends T> adapterType) {
+                return AdapterUtils.tryGetAdapter(adapters, adapterType);
         }
 
         @Override
-        public <T extends ModelStoreAdapter> T getAdapter(ModelAdapterType<?, T, ?> adapterType) {
-                return adapters.get(adapterType, adapterType.getModelStoreAdapterClass());
+        public <T extends ModelStoreAdapter> T getAdapter(Class<T> adapterType) {
+                return AdapterUtils.getAdapter(adapters, adapterType);
         }
 
-        void addAdapter(AnyModelAdapterType adapterType, ModelStoreAdapter adapter) {
-                adapters.add(adapterType, adapter);
+        void addAdapter(ModelStoreAdapter adapter) {
+                adapters.add(adapter);
         }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/SymbolEquivalenceClass.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/SymbolEquivalenceClass.java
index 5bf1b90d..136f2976 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/SymbolEquivalenceClass.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/SymbolEquivalenceClass.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
 import tools.refinery.store.representation.Symbol;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/model/internal/VersionedInterpretation.java b/subprojects/store/src/main/java/tools/refinery/store/model/internal/VersionedInterpretation.java
index c850d334..404be65f 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/model/internal/VersionedInterpretation.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/model/internal/VersionedInterpretation.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.internal;
 
 import tools.refinery.store.map.Cursor;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretation.java b/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretation.java
deleted file mode 100644
index 331fa294..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretation.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package tools.refinery.store.partial;
-
-import tools.refinery.store.adapter.ModelAdapterBuilderFactory;
-import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.partial.internal.PartialInterpretationBuilderImpl;
-
-public final class PartialInterpretation extends ModelAdapterBuilderFactory<PartialInterpretationAdapter,
-                PartialInterpretationStoreAdapter, PartialInterpretationBuilder> {
-        public static final PartialInterpretation ADAPTER = new PartialInterpretation();
-
-        private PartialInterpretation() {
-                super(PartialInterpretationAdapter.class, PartialInterpretationStoreAdapter.class, PartialInterpretationBuilder.class);
-        }
-
-        @Override
-        public PartialInterpretationBuilder createBuilder(ModelStoreBuilder storeBuilder) {
-                return new PartialInterpretationBuilderImpl(storeBuilder);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationAdapter.java
deleted file mode 100644
index 2c83a200..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationAdapter.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.partial;
-
-import tools.refinery.store.adapter.ModelAdapter;
-
-public interface PartialInterpretationAdapter extends ModelAdapter {
-        @Override
-        PartialInterpretationStoreAdapter getStoreAdapter();
-}
-
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationBuilder.java
deleted file mode 100644
index 0ec13836..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationBuilder.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.partial;
-
-import tools.refinery.store.adapter.ModelAdapterBuilder;
-import tools.refinery.store.model.ModelStore;
-
-public interface PartialInterpretationBuilder extends ModelAdapterBuilder {
-        @Override
-        PartialInterpretationStoreAdapter createStoreAdapter(ModelStore store);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationStoreAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationStoreAdapter.java
deleted file mode 100644
index d4eb770d..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/PartialInterpretationStoreAdapter.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.partial;
-
-import tools.refinery.store.adapter.ModelStoreAdapter;
-import tools.refinery.store.model.Model;
-
-public interface PartialInterpretationStoreAdapter extends ModelStoreAdapter {
-        @Override
-        PartialInterpretationAdapter createModelAdapter(Model model);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationAdapterImpl.java b/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationAdapterImpl.java
deleted file mode 100644
index 4b3977c0..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationAdapterImpl.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package tools.refinery.store.partial.internal;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.partial.PartialInterpretationAdapter;
-
-public class PartialInterpretationAdapterImpl implements PartialInterpretationAdapter {
-        private final Model model;
-        private final PartialInterpretationStoreAdapterImpl storeAdapter;
-
-        PartialInterpretationAdapterImpl(Model model, PartialInterpretationStoreAdapterImpl storeAdapter) {
-                this.model = model;
-                this.storeAdapter = storeAdapter;
-        }
-
-        @Override
-        public Model getModel() {
-                return model;
-        }
-
-        @Override
-        public PartialInterpretationStoreAdapterImpl getStoreAdapter() {
-                return storeAdapter;
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationBuilderImpl.java b/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationBuilderImpl.java
deleted file mode 100644
index 4609dc32..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationBuilderImpl.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package tools.refinery.store.partial.internal;
-
-import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
-import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.partial.PartialInterpretationBuilder;
-
-public class PartialInterpretationBuilderImpl extends AbstractModelAdapterBuilder implements PartialInterpretationBuilder {
-        public PartialInterpretationBuilderImpl(ModelStoreBuilder storeBuilder) {
-                super(storeBuilder);
-        }
-
-        @Override
-        public PartialInterpretationStoreAdapterImpl createStoreAdapter(ModelStore store) {
-                return null;
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationStoreAdapterImpl.java b/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationStoreAdapterImpl.java
deleted file mode 100644
index 970b802b..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/partial/internal/PartialInterpretationStoreAdapterImpl.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package tools.refinery.store.partial.internal;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.partial.PartialInterpretationStoreAdapter;
-
-public class PartialInterpretationStoreAdapterImpl implements PartialInterpretationStoreAdapter {
-        private final ModelStore store;
-
-        PartialInterpretationStoreAdapterImpl(ModelStore store) {
-                this.store = store;
-        }
-
-        @Override
-        public ModelStore getStore() {
-                return store;
-        }
-
-        @Override
-        public PartialInterpretationAdapterImpl createModelAdapter(Model model) {
-                return new PartialInterpretationAdapterImpl(model, this);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNF.java b/subprojects/store/src/main/java/tools/refinery/store/query/DNF.java
deleted file mode 100644
index 95c5d787..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNF.java
+++ /dev/null
@@ -1,169 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.query.atom.DNFAtom;
-
-import java.util.*;
-
-public final class DNF implements RelationLike {
-        private final String name;
-
-        private final String uniqueName;
-
-        private final List<Variable> parameters;
-
-        private final List<FunctionalDependency<Variable>> functionalDependencies;
-
-        private final List<DNFAnd> clauses;
-
-        private DNF(String name, List<Variable> parameters, List<FunctionalDependency<Variable>> functionalDependencies,
-                                List<DNFAnd> clauses) {
-                validateFunctionalDependencies(parameters, functionalDependencies);
-                this.name = name;
-                this.uniqueName = DNFUtils.generateUniqueName(name);
-                this.parameters = parameters;
-                this.functionalDependencies = functionalDependencies;
-                this.clauses = clauses;
-        }
-
-        private static void validateFunctionalDependencies(
-                        Collection<Variable> parameters, Collection<FunctionalDependency<Variable>> functionalDependencies) {
-                var parameterSet = new HashSet<>(parameters);
-                for (var functionalDependency : functionalDependencies) {
-                        validateParameters(parameters, parameterSet, functionalDependency.forEach(), functionalDependency);
-                        validateParameters(parameters, parameterSet, functionalDependency.unique(), functionalDependency);
-                }
-        }
-
-        private static void validateParameters(Collection<Variable> parameters, Set<Variable> parameterSet,
-                                                                                   Collection<Variable> toValidate,
-                                                                                   FunctionalDependency<Variable> functionalDependency) {
-                for (var variable : toValidate) {
-                        if (!parameterSet.contains(variable)) {
-                                throw new IllegalArgumentException(
-                                                "Variable %s of functional dependency %s does not appear in the parameter list %s"
-                                                                .formatted(variable, functionalDependency, parameters));
-                        }
-                }
-        }
-
-        @Override
-        public String name() {
-                return name;
-        }
-
-        public String getUniqueName() {
-                return uniqueName;
-        }
-
-        public List<Variable> getParameters() {
-                return parameters;
-        }
-
-        public List<FunctionalDependency<Variable>> getFunctionalDependencies() {
-                return functionalDependencies;
-        }
-
-        @Override
-        public int arity() {
-                return parameters.size();
-        }
-
-        public List<DNFAnd> getClauses() {
-                return clauses;
-        }
-
-        public static Builder builder() {
-                return builder(null);
-        }
-
-        public static Builder builder(String name) {
-                return new Builder(name);
-        }
-
-        @SuppressWarnings("UnusedReturnValue")
-        public static class Builder {
-                private final String name;
-
-                private final List<Variable> parameters = new ArrayList<>();
-
-                private final List<FunctionalDependency<Variable>> functionalDependencies = new ArrayList<>();
-
-                private final List<List<DNFAtom>> clauses = new ArrayList<>();
-
-                private Builder(String name) {
-                        this.name = name;
-                }
-
-                public Builder parameter(Variable variable) {
-                        parameters.add(variable);
-                        return this;
-                }
-
-                public Builder parameters(Variable... variables) {
-                        return parameters(List.of(variables));
-                }
-
-                public Builder parameters(Collection<Variable> variables) {
-                        parameters.addAll(variables);
-                        return this;
-                }
-
-                public Builder functionalDependencies(Collection<FunctionalDependency<Variable>> functionalDependencies) {
-                        this.functionalDependencies.addAll(functionalDependencies);
-                        return this;
-                }
-
-                public Builder functionalDependency(FunctionalDependency<Variable> functionalDependency) {
-                        functionalDependencies.add(functionalDependency);
-                        return this;
-                }
-
-                public Builder functionalDependency(Set<Variable> forEach, Set<Variable> unique) {
-                        return functionalDependency(new FunctionalDependency<>(forEach, unique));
-                }
-
-                public Builder clause(DNFAtom... atoms) {
-                        clauses.add(List.of(atoms));
-                        return this;
-                }
-
-                public Builder clause(Collection<DNFAtom> atoms) {
-                        clauses.add(List.copyOf(atoms));
-                        return this;
-                }
-
-                public Builder clause(DNFAnd clause) {
-                        return clause(clause.constraints());
-                }
-
-                public Builder clauses(DNFAnd... clauses) {
-                        for (var clause : clauses) {
-                                this.clause(clause);
-                        }
-                        return this;
-                }
-
-                public Builder clauses(Collection<DNFAnd> clauses) {
-                        for (var clause : clauses) {
-                                this.clause(clause);
-                        }
-                        return this;
-                }
-
-                public DNF build() {
-                        var postProcessedClauses = new ArrayList<DNFAnd>();
-                        for (var constraints : clauses) {
-                                var variables = new HashSet<Variable>();
-                                for (var constraint : constraints) {
-                                        constraint.collectAllVariables(variables);
-                                }
-                                parameters.forEach(variables::remove);
-                                postProcessedClauses.add(new DNFAnd(Collections.unmodifiableSet(variables),
-                                                Collections.unmodifiableList(constraints)));
-                        }
-                        return new DNF(name, Collections.unmodifiableList(parameters),
-                                        Collections.unmodifiableList(functionalDependencies),
-                                        Collections.unmodifiableList(postProcessedClauses));
-                }
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java b/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java
deleted file mode 100644
index 8c3bf05d..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/DNFAnd.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.query.atom.DNFAtom;
-
-import java.util.List;
-import java.util.Set;
-
-public record DNFAnd(Set<Variable> quantifiedVariables, List<DNFAtom> constraints) {
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQuery.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQuery.java
deleted file mode 100644
index 6a1aeabb..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQuery.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.adapter.ModelAdapterType;
-
-public final class ModelQuery extends ModelAdapterType<ModelQueryAdapter, ModelQueryStoreAdapter, ModelQueryBuilder> {
-        public static final ModelQuery ADAPTER = new ModelQuery();
-
-        private ModelQuery() {
-                super(ModelQueryAdapter.class, ModelQueryStoreAdapter.class, ModelQueryBuilder.class);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
deleted file mode 100644
index 7449e39b..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.adapter.ModelAdapter;
-
-public interface ModelQueryAdapter extends ModelAdapter {
-        ModelQueryStoreAdapter getStoreAdapter();
-
-        ResultSet getResultSet(DNF query);
-
-        boolean hasPendingChanges();
-
-        void flushChanges();
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
deleted file mode 100644
index 4364d844..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.adapter.ModelAdapterBuilder;
-import tools.refinery.store.model.ModelStore;
-
-import java.util.Collection;
-import java.util.List;
-
-public interface ModelQueryBuilder extends ModelAdapterBuilder {
-        default ModelQueryBuilder queries(DNF... queries) {
-                return queries(List.of(queries));
-        }
-
-        default ModelQueryBuilder queries(Collection<DNF> queries) {
-                queries.forEach(this::query);
-                return this;
-        }
-
-        ModelQueryBuilder query(DNF query);
-
-        @Override
-        ModelQueryStoreAdapter createStoreAdapter(ModelStore store);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java b/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
deleted file mode 100644
index ef5a4587..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.adapter.ModelStoreAdapter;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.view.AnyRelationView;
-
-import java.util.Collection;
-
-public interface ModelQueryStoreAdapter extends ModelStoreAdapter {
-        Collection<AnyRelationView> getRelationViews();
-
-        Collection<DNF> getQueries();
-
-        @Override
-        ModelQueryAdapter createModelAdapter(Model model);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/RelationLike.java b/subprojects/store/src/main/java/tools/refinery/store/query/RelationLike.java
deleted file mode 100644
index 8c784d8b..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/RelationLike.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package tools.refinery.store.query;
-
-public interface RelationLike {
-        String name();
-
-        int arity();
-
-        default boolean invalidIndex(int i) {
-                return i < 0 || i >= arity();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/ResultSet.java b/subprojects/store/src/main/java/tools/refinery/store/query/ResultSet.java
deleted file mode 100644
index 3542e252..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/ResultSet.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package tools.refinery.store.query;
-
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.TupleLike;
-
-import java.util.Optional;
-import java.util.stream.Stream;
-
-public interface ResultSet {
-        boolean hasResult();
-
-        boolean hasResult(Tuple parameters);
-
-        Optional<TupleLike> oneResult();
-
-        Optional<TupleLike> oneResult(Tuple parameters);
-
-        Stream<TupleLike> allResults();
-
-        Stream<TupleLike> allResults(Tuple parameters);
-
-        int countResults();
-
-        int countResults(Tuple parameters);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java b/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java
deleted file mode 100644
index 3632f3c5..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/Variable.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package tools.refinery.store.query;
-
-import java.util.Objects;
-
-public class Variable {
-        private final String name;
-        private final String uniqueName;
-
-        public Variable() {
-                this(null);
-        }
-
-        public Variable(String name) {
-                super();
-                this.name = name;
-                this.uniqueName = DNFUtils.generateUniqueName(name);
-
-        }
-        public String getName() {
-                return name;
-        }
-
-        public String getUniqueName() {
-                return uniqueName;
-        }
-
-        public boolean isNamed() {
-                return name != null;
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                Variable variable = (Variable) o;
-                return Objects.equals(uniqueName, variable.uniqueName);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(uniqueName);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallAtom.java
deleted file mode 100644
index 47121870..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/CallAtom.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.RelationLike;
-
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-
-public abstract class CallAtom<T extends RelationLike> implements DNFAtom {
-        private final CallPolarity polarity;
-        private final T target;
-        private final List<Variable> substitution;
-
-        protected CallAtom(CallPolarity polarity, T target, List<Variable> substitution) {
-                if (substitution.size() != target.arity()) {
-                        throw new IllegalArgumentException("%s needs %d arguments, but got %s".formatted(target.name(),
-                                        target.arity(), substitution.size()));
-                }
-                if (polarity.isTransitive() && target.arity() != 2) {
-                        throw new IllegalArgumentException("Transitive closures can only take binary relations");
-                }
-                this.polarity = polarity;
-                this.target = target;
-                this.substitution = substitution;
-        }
-
-        protected CallAtom(CallPolarity polarity, T target, Variable... substitution) {
-                this(polarity, target, List.of(substitution));
-        }
-
-        protected CallAtom(boolean positive, T target, List<Variable> substitution) {
-                this(CallPolarity.fromBoolean(positive), target, substitution);
-        }
-
-        protected CallAtom(boolean positive, T target, Variable... substitution) {
-                this(positive, target, List.of(substitution));
-        }
-
-        protected CallAtom(T target, List<Variable> substitution) {
-                this(true, target, substitution);
-        }
-
-        protected CallAtom(T target, Variable... substitution) {
-                this(target, List.of(substitution));
-        }
-
-        public CallPolarity getPolarity() {
-                return polarity;
-        }
-
-        public T getTarget() {
-                return target;
-        }
-
-        public List<Variable> getSubstitution() {
-                return substitution;
-        }
-
-        @Override
-        public void collectAllVariables(Set<Variable> variables) {
-                if (polarity.isPositive()) {
-                        variables.addAll(substitution);
-                }
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                CallAtom<?> callAtom = (CallAtom<?>) o;
-                return polarity == callAtom.polarity && Objects.equals(target, callAtom.target) && Objects.equals(substitution
-                                , callAtom.substitution);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(polarity, target, substitution);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/ConstantAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/ConstantAtom.java
deleted file mode 100644
index 13dae7d0..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/ConstantAtom.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-
-import java.util.Set;
-
-public record ConstantAtom(Variable variable, int nodeId) implements DNFAtom {
-        @Override
-        public void collectAllVariables(Set<Variable> variables) {
-                variables.add(variable);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFAtom.java
deleted file mode 100644
index ebf71236..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFAtom.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-
-import java.util.Set;
-
-public interface DNFAtom {
-        void collectAllVariables(Set<Variable> variables);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java
deleted file mode 100644
index 3b4f5cd1..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/DNFCallAtom.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.DNF;
-import tools.refinery.store.query.Variable;
-
-import java.util.List;
-
-public class DNFCallAtom extends CallAtom<DNF> {
-        public DNFCallAtom(CallPolarity polarity, DNF target, List<Variable> substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public DNFCallAtom(CallPolarity polarity, DNF target, Variable... substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public DNFCallAtom(boolean positive, DNF target, List<Variable> substitution) {
-                super(positive, target, substitution);
-        }
-
-        public DNFCallAtom(boolean positive, DNF target, Variable... substitution) {
-                super(positive, target, substitution);
-        }
-
-        public DNFCallAtom(DNF target, List<Variable> substitution) {
-                super(target, substitution);
-        }
-
-        public DNFCallAtom(DNF target, Variable... substitution) {
-                super(target, substitution);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/EquivalenceAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/EquivalenceAtom.java
deleted file mode 100644
index b1b3a6f7..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/EquivalenceAtom.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-
-import java.util.Set;
-
-public record EquivalenceAtom(boolean positive, Variable left, Variable right) implements DNFAtom {
-        public EquivalenceAtom(Variable left, Variable right) {
-                this(true, left, right);
-        }
-
-        @Override
-        public void collectAllVariables(Set<Variable> variables) {
-                variables.add(left);
-                variables.add(right);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/Modality.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/Modality.java
deleted file mode 100644
index e389f563..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/Modality.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import java.util.Locale;
-
-public enum Modality {
-        MUST,
-        MAY,
-        CURRENT;
-
-        public Modality negate() {
-                return switch(this) {
-                        case MUST -> MAY;
-                        case MAY -> MUST;
-                        case CURRENT -> CURRENT;
-                };
-        }
-
-        @Override
-        public String toString() {
-                return name().toLowerCase(Locale.ROOT);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java b/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java
deleted file mode 100644
index a2b176c4..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/atom/RelationViewAtom.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package tools.refinery.store.query.atom;
-
-import tools.refinery.store.query.Variable;
-import tools.refinery.store.query.view.AnyRelationView;
-
-import java.util.List;
-
-public final class RelationViewAtom extends CallAtom<AnyRelationView> {
-        public RelationViewAtom(CallPolarity polarity, AnyRelationView target, List<Variable> substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public RelationViewAtom(CallPolarity polarity, AnyRelationView target, Variable... substitution) {
-                super(polarity, target, substitution);
-        }
-
-        public RelationViewAtom(boolean positive, AnyRelationView target, List<Variable> substitution) {
-                super(positive, target, substitution);
-        }
-
-        public RelationViewAtom(boolean positive, AnyRelationView target, Variable... substitution) {
-                super(positive, target, substitution);
-        }
-
-        public RelationViewAtom(AnyRelationView target, List<Variable> substitution) {
-                super(target, substitution);
-        }
-
-        public RelationViewAtom(AnyRelationView target, Variable... substitution) {
-                super(target, substitution);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/AnyRelationView.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/AnyRelationView.java
deleted file mode 100644
index 328cde3a..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/AnyRelationView.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package tools.refinery.store.query.view;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.FunctionalDependency;
-import tools.refinery.store.representation.AnySymbol;
-import tools.refinery.store.query.RelationLike;
-
-import java.util.Set;
-
-public sealed interface AnyRelationView extends RelationLike permits RelationView {
-        AnySymbol getSymbol();
-
-        default Set<FunctionalDependency<Integer>> getFunctionalDependencies() {
-                return Set.of();
-        }
-
-        default Set<RelationViewImplication> getImpliedRelationViews() {
-                return Set.of();
-        }
-
-        boolean get(Model model, Object[] tuple);
-
-        Iterable<Object[]> getAll(Model model);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/FilteredRelationView.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/FilteredRelationView.java
deleted file mode 100644
index 64c601bb..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/FilteredRelationView.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package tools.refinery.store.query.view;
-
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.Objects;
-import java.util.function.BiPredicate;
-import java.util.function.Predicate;
-
-public class FilteredRelationView<T> extends TuplePreservingRelationView<T> {
-        private final BiPredicate<Tuple, T> predicate;
-
-        public FilteredRelationView(Symbol<T> symbol, String name, BiPredicate<Tuple, T> predicate) {
-                super(symbol, name);
-                this.predicate = predicate;
-        }
-
-        public FilteredRelationView(Symbol<T> symbol, BiPredicate<Tuple, T> predicate) {
-                super(symbol);
-                this.predicate = predicate;
-        }
-
-        public FilteredRelationView(Symbol<T> symbol, String name, Predicate<T> predicate) {
-                this(symbol, name, (k, v) -> predicate.test(v));
-        }
-
-        public FilteredRelationView(Symbol<T> symbol, Predicate<T> predicate) {
-                this(symbol, (k, v) -> predicate.test(v));
-        }
-
-        @Override
-        public boolean filter(Tuple key, T value) {
-                return this.predicate.test(key, value);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                if (!super.equals(o)) return false;
-                FilteredRelationView<?> that = (FilteredRelationView<?>) o;
-                return Objects.equals(predicate, that.predicate);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(super.hashCode(), predicate);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/FunctionalRelationView.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/FunctionalRelationView.java
deleted file mode 100644
index 3d278a8b..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/FunctionalRelationView.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package tools.refinery.store.query.view;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.FunctionalDependency;
-import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple1;
-
-import java.util.Set;
-import java.util.stream.Collectors;
-import java.util.stream.IntStream;
-
-public final class FunctionalRelationView<T> extends RelationView<T> {
-        public FunctionalRelationView(Symbol<T> symbol, String name) {
-                super(symbol, name);
-        }
-
-        public FunctionalRelationView(Symbol<T> symbol) {
-                super(symbol);
-        }
-
-        @Override
-        public Set<FunctionalDependency<Integer>> getFunctionalDependencies() {
-                var arity = getSymbol().arity();
-                var forEach = IntStream.range(0, arity).boxed().collect(Collectors.toUnmodifiableSet());
-                var unique = Set.of(arity);
-                return Set.of(new FunctionalDependency<>(forEach, unique));
-        }
-
-        @Override
-        public Set<RelationViewImplication> getImpliedRelationViews() {
-                var symbol = getSymbol();
-                var impliedIndices = IntStream.range(0, symbol.arity()).boxed().toList();
-                var keyOnlyRelationView = new KeyOnlyRelationView<>(symbol);
-                return Set.of(new RelationViewImplication(this, keyOnlyRelationView, impliedIndices));
-        }
-
-        @Override
-        public boolean filter(Tuple key, T value) {
-                return true;
-        }
-
-        @Override
-        public Object[] forwardMap(Tuple key, T value) {
-                int size = key.getSize();
-                Object[] result = new Object[size + 1];
-                for (int i = 0; i < size; i++) {
-                        result[i] = Tuple.of(key.get(i));
-                }
-                result[key.getSize()] = value;
-                return result;
-        }
-
-        @Override
-        public boolean get(Model model, Object[] tuple) {
-                int[] content = new int[tuple.length - 1];
-                for (int i = 0; i < tuple.length - 1; i++) {
-                        content[i] = ((Tuple1) tuple[i]).value0();
-                }
-                Tuple key = Tuple.of(content);
-                @SuppressWarnings("unchecked")
-                T valueInTuple = (T) tuple[tuple.length - 1];
-                T valueInMap = model.getInterpretation(getSymbol()).get(key);
-                return valueInTuple.equals(valueInMap);
-        }
-
-        @Override
-        public int arity() {
-                return getSymbol().arity() + 1;
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationView.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationView.java
deleted file mode 100644
index bbec1e73..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationView.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package tools.refinery.store.query.view;
-
-import tools.refinery.store.map.CursorAsIterator;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.tuple.Tuple;
-
-import java.util.Objects;
-import java.util.UUID;
-
-/**
- * Represents a view of a {@link Symbol} that can be queried.
- *
- * @param <T>
- * @author Oszkar Semerath
- */
-public abstract non-sealed class RelationView<T> implements AnyRelationView {
-        private final Symbol<T> symbol;
-
-        private final String name;
-
-        protected RelationView(Symbol<T> symbol, String name) {
-                this.symbol = symbol;
-                this.name = name;
-        }
-
-        protected RelationView(Symbol<T> representation) {
-                this(representation, UUID.randomUUID().toString());
-        }
-
-        @Override
-        public Symbol<T> getSymbol() {
-                return symbol;
-        }
-
-        @Override
-        public String name() {
-                return symbol.name() + "#" + name;
-        }
-
-        public abstract boolean filter(Tuple key, T value);
-
-        public abstract Object[] forwardMap(Tuple key, T value);
-
-        @Override
-        public Iterable<Object[]> getAll(Model model) {
-                return (() -> new CursorAsIterator<>(model.getInterpretation(symbol).getAll(), this::forwardMap, this::filter));
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                RelationView<?> that = (RelationView<?>) o;
-                return Objects.equals(symbol, that.symbol) && Objects.equals(name, that.name);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(symbol, name);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationViewImplication.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationViewImplication.java
deleted file mode 100644
index 2ba1fcc4..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/RelationViewImplication.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package tools.refinery.store.query.view;
-
-import java.util.List;
-
-public record RelationViewImplication(AnyRelationView implyingRelationView, AnyRelationView impliedRelationView,
-                                                                          List<Integer> impliedIndices) {
-        public RelationViewImplication {
-                if (impliedIndices.size() != impliedRelationView.arity()) {
-                        throw new IllegalArgumentException("Expected %d implied indices for %s, but %d are provided"
-                                        .formatted(impliedRelationView.arity(), impliedRelationView, impliedIndices.size()));
-                }
-                for (var index : impliedIndices) {
-                        if (impliedRelationView.invalidIndex(index)) {
-                                throw new IllegalArgumentException("%d is not a valid index for %s".formatted(index,
-                                                implyingRelationView));
-                        }
-                }
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/query/view/TuplePreservingRelationView.java b/subprojects/store/src/main/java/tools/refinery/store/query/view/TuplePreservingRelationView.java
deleted file mode 100644
index 8cc4986e..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/query/view/TuplePreservingRelationView.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package tools.refinery.store.query.view;
-
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple1;
-import tools.refinery.store.representation.Symbol;
-
-public abstract class TuplePreservingRelationView<T> extends RelationView<T> {
-        protected TuplePreservingRelationView(Symbol<T> symbol, String name) {
-                super(symbol, name);
-        }
-
-        protected TuplePreservingRelationView(Symbol<T> symbol) {
-                super(symbol);
-        }
-
-        public Object[] forwardMap(Tuple key) {
-                Object[] result = new Object[key.getSize()];
-                for (int i = 0; i < key.getSize(); i++) {
-                        result[i] = Tuple.of(key.get(i));
-                }
-                return result;
-        }
-
-        @Override
-        public Object[] forwardMap(Tuple key, T value) {
-                return forwardMap(key);
-        }
-
-        @Override
-        public boolean get(Model model, Object[] tuple) {
-                int[] content = new int[tuple.length];
-                for (int i = 0; i < tuple.length; i++) {
-                        content[i] = ((Tuple1) tuple[i]).value0();
-                }
-                Tuple key = Tuple.of(content);
-                T value = model.getInterpretation(getSymbol()).get(key);
-                return filter(key, value);
-        }
-
-        public int arity() {
-                return this.getSymbol().arity();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.java
new file mode 100644
index 00000000..52c740e8
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.java
@@ -0,0 +1,34 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.representation;
+
+import java.util.Optional;
+
+public non-sealed interface AbstractDomain<A, C> extends AnyAbstractDomain {
+        @Override
+        Class<A> abstractType();
+
+        @Override
+        Class<C> concreteType();
+
+        A toAbstract(C concreteValue);
+
+        Optional<C> toConcrete(A abstractValue);
+
+        default boolean isConcrete(A abstractValue) {
+                return toConcrete(abstractValue).isPresent();
+        }
+
+        boolean isRefinement(A originalValue, A refinedValue);
+
+        A commonRefinement(A leftValue, A rightValue);
+
+        A commonAncestor(A leftValue, A rightValue);
+
+        A unknown();
+
+        boolean isError(A abstractValue);
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java
new file mode 100644
index 00000000..c354fab7
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java
@@ -0,0 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.representation;
+
+public sealed interface AnyAbstractDomain permits AbstractDomain {
+        Class<?> abstractType();
+
+        Class<?> concreteType();
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/AnySymbol.java b/subprojects/store/src/main/java/tools/refinery/store/representation/AnySymbol.java
index 20b9eead..b2377905 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/AnySymbol.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/AnySymbol.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation;
 
 public sealed interface AnySymbol permits Symbol {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java b/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
index 85ea15f4..cc748180 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/Symbol.java
@@ -1,25 +1,25 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation;
 
-import java.util.Objects;
-
 public record Symbol<T>(String name, int arity, Class<T> valueType, T defaultValue) implements AnySymbol {
-        public boolean isDefaultValue(T value) {
-                return Objects.equals(defaultValue, value);
+        @Override
+        public String toString() {
+                return "%s/%d".formatted(name, arity);
         }
 
-        @Override
-        public boolean equals(Object o) {
-                return this == o;
+        public static Symbol<Boolean> of(String name, int arity) {
+                return of(name, arity, Boolean.class, false);
         }
 
-        @Override
-        public int hashCode() {
-                // Compare by identity to make hash table lookups more efficient.
-                return System.identityHashCode(this);
+        public static <T> Symbol<T> of(String name, int arity, Class<T> valueType) {
+                return of(name, arity, valueType, null);
         }
 
-        @Override
-        public String toString() {
-                return "%s/%d".formatted(name, arity);
+        public static <T> Symbol<T> of(String name, int arity, Class<T> valueType, T defaultValue) {
+                return new Symbol<>(name, arity, valueType, defaultValue);
         }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java
index b7893fd3..40baf9a5 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation;
 
 public enum TruthValue {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java
new file mode 100644
index 00000000..89f8dd19
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.representation;
+
+import java.util.Optional;
+
+public final class TruthValueDomain implements AbstractDomain<TruthValue, Boolean> {
+        public static final TruthValueDomain INSTANCE = new TruthValueDomain();
+
+        private TruthValueDomain() {
+        }
+
+        @Override
+        public Class<TruthValue> abstractType() {
+                return null;
+        }
+
+        @Override
+        public Class<Boolean> concreteType() {
+                return null;
+        }
+
+        @Override
+        public TruthValue toAbstract(Boolean concreteValue) {
+                return null;
+        }
+
+        @Override
+        public Optional<Boolean> toConcrete(TruthValue abstractValue) {
+                return Optional.empty();
+        }
+
+        @Override
+        public boolean isConcrete(TruthValue abstractValue) {
+                return AbstractDomain.super.isConcrete(abstractValue);
+        }
+
+        @Override
+        public boolean isRefinement(TruthValue originalValue, TruthValue refinedValue) {
+                return false;
+        }
+
+        @Override
+        public TruthValue commonRefinement(TruthValue leftValue, TruthValue rightValue) {
+                return null;
+        }
+
+        @Override
+        public TruthValue commonAncestor(TruthValue leftValue, TruthValue rightValue) {
+                return null;
+        }
+
+        @Override
+        public TruthValue unknown() {
+                return null;
+        }
+
+        @Override
+        public boolean isError(TruthValue abstractValue) {
+                return false;
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java
index 273d0de7..704ca2fc 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 public sealed interface CardinalityInterval permits NonEmptyCardinalityInterval, EmptyCardinalityInterval {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java
index e1a08bf9..ad16a3e8 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 public final class CardinalityIntervals {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java
index ab3ad9d1..49911c29 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 public final class EmptyCardinalityInterval implements CardinalityInterval {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java
index 381c8a57..82afdbbc 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.jetbrains.annotations.NotNull;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java
index 32b3786f..38bd53bf 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import java.util.function.BinaryOperator;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java
index 593bc322..a5634020 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.jetbrains.annotations.NotNull;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java
index d850fdc9..1e18dde0 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 public final class UpperCardinalities {
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java
index c6e31cb7..5dbaa922 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 public sealed interface UpperCardinality extends Comparable<UpperCardinality> permits FiniteUpperCardinality,
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple.java
index bf844c6d..aae7b344 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple.java
@@ -1,28 +1,60 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.tuple;
 
-public sealed interface Tuple extends TupleLike permits Tuple0, Tuple1, Tuple2, TupleN {
+import org.jetbrains.annotations.NotNull;
+
+public sealed interface Tuple extends Comparable<Tuple> permits Tuple0, Tuple1, Tuple2, Tuple3, Tuple4, TupleN {
+        int getSize();
+
+        int get(int element);
+
         @Override
-        default Tuple toTuple() {
-                return this;
+        default int compareTo(@NotNull Tuple other) {
+                int size = getSize();
+                int compareSize = Integer.compare(size, other.getSize());
+                if (compareSize != 0) {
+                        return compareSize;
+                }
+                for (int i = 0; i < size; i++) {
+                        int compareElement = Integer.compare(get(i), other.get(i));
+                        if (compareElement != 0) {
+                                return compareElement;
+                        }
+                }
+                return 0;
         }
 
-        static Tuple of() {
+        static Tuple0 of() {
                 return Tuple0.INSTANCE;
         }
 
-        static Tuple of(int value) {
+        static Tuple1 of(int value) {
                 return Tuple1.Cache.INSTANCE.getOrCreate(value);
         }
 
-        static Tuple of(int value1, int value2) {
+        static Tuple2 of(int value1, int value2) {
                 return new Tuple2(value1, value2);
         }
 
+        static Tuple3 of(int value1, int value2, int value3) {
+                return new Tuple3(value1, value2, value3);
+        }
+
+        static Tuple4 of(int value1, int value2, int value3, int value4) {
+                return new Tuple4(value1, value2, value3, value4);
+        }
+
         static Tuple of(int... values) {
                 return switch (values.length) {
                         case 0 -> of();
                         case 1 -> of(values[0]);
                         case 2 -> of(values[0], values[1]);
+                        case 3 -> of(values[0], values[1], values[2]);
+                        case 4 -> of(values[0], values[1], values[2], values[3]);
                         default -> new TupleN(values);
                 };
         }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple0.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple0.java
index 8eea5c3a..a9aa9bf2 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple0.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple0.java
@@ -1,7 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.tuple;
 
-public record Tuple0() implements Tuple {
-        public static Tuple0 INSTANCE = new Tuple0();
+import static tools.refinery.store.tuple.TupleConstants.TUPLE_BEGIN;
+import static tools.refinery.store.tuple.TupleConstants.TUPLE_END;
+
+/**
+ * Singleton implementation to ensure only a single empty tuple exists.
+ */
+@SuppressWarnings("squid:S6548")
+public final class Tuple0 implements Tuple {
+        public static final Tuple0 INSTANCE = new Tuple0();
+
+        private Tuple0() {
+        }
 
         @Override
         public int getSize() {
@@ -14,12 +29,7 @@ public record Tuple0() implements Tuple {
         }
 
         @Override
-        public int[] toArray() {
-                return new int[]{};
-        }
-
-        @Override
         public String toString() {
-                return "[]";
+                return TUPLE_BEGIN + TUPLE_END;
         }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple1.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple1.java
index 07380966..388ee3a9 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple1.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple1.java
@@ -1,10 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.tuple;
 
+import org.jetbrains.annotations.NotNull;
 import tools.refinery.store.model.TupleHashProvider;
 
 import java.util.Arrays;
 
-public record Tuple1(int value0) implements Tuple {
+import static tools.refinery.store.tuple.TupleConstants.TUPLE_BEGIN;
+import static tools.refinery.store.tuple.TupleConstants.TUPLE_END;
+
+public final class Tuple1 implements Tuple {
+        private final int value0;
+
+        private Tuple1(int value0) {
+                this.value0 = value0;
+        }
+
+        public int value0() {
+                return value0;
+        }
+
         @Override
         public int getSize() {
                 return 1;
@@ -19,20 +38,40 @@ public record Tuple1(int value0) implements Tuple {
         }
 
         @Override
-        public int[] toArray() {
-                return new int[]{value0};
+        public String toString() {
+                return TUPLE_BEGIN + value0 + TUPLE_END;
         }
 
         @Override
-        public String toString() {
-                return "[" + value0 + "]";
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Tuple1 tuple1 = (Tuple1) o;
+                return value0 == tuple1.value0;
+        }
+
+        @Override
+        public int hashCode() {
+                return 31 + value0;
+        }
+
+        @Override
+        public int compareTo(@NotNull Tuple other) {
+                if (other instanceof Tuple1 other1) {
+                        return Integer.compare(value0, other1.value0);
+                }
+                return Tuple.super.compareTo(other);
         }
 
         /**
          * This class uses safe double-checked locking, see
          * <a href="https://shipilev.net/blog/2014/safe-public-construction/">Safe Publication and Safe Initialization in
          * Java</a> for details.
+         * <p>
+         * This class implements the singleton pattern to ensure only a single cache exists. This is thread-safe because
+         * of the locking of the cache.
          */
+        @SuppressWarnings("squid:S6548")
         public static class Cache {
                 private static final int MIN_CACHE_SIZE = 256;
 
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple2.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple2.java
index 0836a32d..6d886fd3 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple2.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple2.java
@@ -1,5 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.tuple;
 
+import org.jetbrains.annotations.NotNull;
+
+import static tools.refinery.store.tuple.TupleConstants.*;
+
 public record Tuple2(int value0, int value1) implements Tuple {
         @Override
         public int getSize() {
@@ -16,12 +25,34 @@ public record Tuple2(int value0, int value1) implements Tuple {
         }
 
         @Override
-        public int[] toArray() {
-                return new int[]{value0, value1};
+        public String toString() {
+                return TUPLE_BEGIN + value0 + TUPLE_SEPARATOR + value1 + TUPLE_END;
         }
 
         @Override
-        public String toString() {
-                return "[" + value0 + ", " + value1 + "]";
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Tuple2 tuple2 = (Tuple2) o;
+                return value0 == tuple2.value0 && value1 == tuple2.value1;
+        }
+
+        @Override
+        public int hashCode() {
+                int hash = 31 + value0;
+                hash = 31 * hash + value1;
+                return hash;
+        }
+
+        @Override
+        public int compareTo(@NotNull Tuple other) {
+                if (other instanceof Tuple2 other2) {
+                        int compare0 = Integer.compare(value0, other2.value0);
+                        if (compare0 != 0) {
+                                return compare0;
+                        }
+                        return Integer.compare(value1, other2.value1);
+                }
+                return Tuple.super.compareTo(other);
         }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple3.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple3.java
new file mode 100644
index 00000000..734e45c2
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple3.java
@@ -0,0 +1,64 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.tuple;
+
+import org.jetbrains.annotations.NotNull;
+
+import static tools.refinery.store.tuple.TupleConstants.*;
+
+public record Tuple3(int value0, int value1, int value2) implements Tuple {
+        @Override
+        public int getSize() {
+                return 3;
+        }
+
+        @Override
+        public int get(int element) {
+                return switch (element) {
+                        case 0 -> value0;
+                        case 1 -> value1;
+                        case 2 -> value2;
+                        default -> throw new ArrayIndexOutOfBoundsException(element);
+                };
+        }
+
+        @Override
+        public String toString() {
+                return TUPLE_BEGIN + value0 + TUPLE_SEPARATOR + value1 + TUPLE_SEPARATOR + value2 + TUPLE_END;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Tuple3 tuple3 = (Tuple3) o;
+                return value0 == tuple3.value0 && value1 == tuple3.value1 && value2 == tuple3.value2;
+        }
+
+        @Override
+        public int hashCode() {
+                int hash = 31 + value0;
+                hash = 31 * hash + value1;
+                hash = 31 * hash + value2;
+                return hash;
+        }
+
+        @Override
+        public int compareTo(@NotNull Tuple other) {
+                if (other instanceof Tuple3 other3) {
+                        int compare0 = Integer.compare(value0, other3.value0);
+                        if (compare0 != 0) {
+                                return compare0;
+                        }
+                        int compare1 = Integer.compare(value1, other3.value1);
+                        if (compare1 != 0) {
+                                return compare1;
+                        }
+                        return Integer.compare(value2, other3.value2);
+                }
+                return Tuple.super.compareTo(other);
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple4.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple4.java
new file mode 100644
index 00000000..e1b93e7b
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/Tuple4.java
@@ -0,0 +1,71 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.tuple;
+
+import org.jetbrains.annotations.NotNull;
+
+import static tools.refinery.store.tuple.TupleConstants.*;
+
+public record Tuple4(int value0, int value1, int value2, int value3) implements Tuple {
+        @Override
+        public int getSize() {
+                return 4;
+        }
+
+        @Override
+        public int get(int element) {
+                return switch (element) {
+                        case 0 -> value0;
+                        case 1 -> value1;
+                        case 2 -> value2;
+                        case 3 -> value3;
+                        default -> throw new ArrayIndexOutOfBoundsException(element);
+                };
+        }
+
+        @Override
+        public String toString() {
+                return TUPLE_BEGIN + value0 + TUPLE_SEPARATOR + value1 + TUPLE_SEPARATOR + value2 + TUPLE_SEPARATOR + value3 +
+                                TUPLE_END;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+                if (this == o) return true;
+                if (o == null || getClass() != o.getClass()) return false;
+                Tuple4 tuple4 = (Tuple4) o;
+                return value0 == tuple4.value0 && value1 == tuple4.value1 && value2 == tuple4.value2 && value3 == tuple4.value3;
+        }
+
+        @Override
+        public int hashCode() {
+                int hash = 31 + value0;
+                hash = 31 * hash + value1;
+                hash = 31 * hash + value2;
+                hash = 31 * hash + value3;
+                return hash;
+        }
+
+        @Override
+        public int compareTo(@NotNull Tuple other) {
+                if (other instanceof Tuple4 other4) {
+                        int compare0 = Integer.compare(value0, other4.value0);
+                        if (compare0 != 0) {
+                                return compare0;
+                        }
+                        int compare1 = Integer.compare(value1, other4.value1);
+                        if (compare1 != 0) {
+                                return compare1;
+                        }
+                        int compare2 = Integer.compare(value2, other4.value2);
+                        if (compare2 != 0) {
+                                return compare2;
+                        }
+                        return Integer.compare(value3, other4.value3);
+                }
+                return Tuple.super.compareTo(other);
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleConstants.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleConstants.java
new file mode 100644
index 00000000..f7d27848
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleConstants.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.tuple;
+
+final class TupleConstants {
+        public static final int MAX_STATIC_ARITY_TUPLE_SIZE = 4;
+        public static final String TUPLE_BEGIN = "[";
+        public static final String TUPLE_SEPARATOR = ", ";
+        public static final String TUPLE_END = "]";
+
+        private TupleConstants() {
+                throw new IllegalArgumentException("This is a static utility class an should not instantiated directly");
+        }
+}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleLike.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleLike.java
deleted file mode 100644
index 470ca298..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleLike.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package tools.refinery.store.tuple;
-
-public interface TupleLike {
-        int getSize();
-
-        int get(int element);
-
-        default int[] toArray() {
-                int size = getSize();
-                var array = new int[size];
-                for (int i = 0; i < size; i++) {
-                        array[i] = get(i);
-                }
-                return array;
-        }
-
-        default Tuple toTuple() {
-                return switch (getSize()) {
-                        case 0 -> Tuple.of();
-                        case 1 -> Tuple.of(get(0));
-                        case 2 -> Tuple.of(get(0), get(1));
-                        default -> Tuple.of(toArray());
-                };
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleN.java b/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleN.java
index 15fd063b..b66af491 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleN.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/tuple/TupleN.java
@@ -1,14 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.tuple;
 
 import java.util.Arrays;
 import java.util.stream.Collectors;
 
-public record TupleN(int[] values) implements Tuple {
-        static final int CUSTOM_TUPLE_SIZE = 2;
+import static tools.refinery.store.tuple.TupleConstants.*;
 
-        public TupleN(int[] values) {
-                if (values.length < CUSTOM_TUPLE_SIZE)
-                        throw new IllegalArgumentException();
+public final class TupleN implements Tuple {
+        private final int[] values;
+
+        TupleN(int[] values) {
+                if (values.length < MAX_STATIC_ARITY_TUPLE_SIZE) {
+                        throw new IllegalArgumentException("Tuples of size at most %d must use static arity Tuple classes"
+                                        .formatted(MAX_STATIC_ARITY_TUPLE_SIZE));
+                }
                 this.values = Arrays.copyOf(values, values.length);
         }
 
@@ -23,19 +32,11 @@ public record TupleN(int[] values) implements Tuple {
         }
 
         @Override
-        public int[] toArray() {
-                return values;
-        }
-
-        @Override
         public String toString() {
-                var valuesString = Arrays.stream(values).mapToObj(Integer::toString).collect(Collectors.joining(", "));
-                return "[" + valuesString + "]";
-        }
-
-        @Override
-        public int hashCode() {
-                return Arrays.hashCode(values);
+                var valuesString = Arrays.stream(values)
+                                .mapToObj(Integer::toString)
+                                .collect(Collectors.joining(TUPLE_SEPARATOR));
+                return TUPLE_BEGIN + valuesString + TUPLE_END;
         }
 
         @Override
@@ -49,4 +50,9 @@ public record TupleN(int[] values) implements Tuple {
                 TupleN other = (TupleN) obj;
                 return Arrays.equals(values, other.values);
         }
+
+        @Override
+        public int hashCode() {
+                return Arrays.hashCode(values);
+        }
 }
diff --git a/subprojects/store/src/main/java/tools/refinery/store/util/CollectionsUtil.java b/subprojects/store/src/main/java/tools/refinery/store/util/CollectionsUtil.java
index 841d0dfa..adecd79b 100644
--- a/subprojects/store/src/main/java/tools/refinery/store/util/CollectionsUtil.java
+++ b/subprojects/store/src/main/java/tools/refinery/store/util/CollectionsUtil.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.util;
 
 import java.util.Iterator;
diff --git a/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java b/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java
new file mode 100644
index 00000000..78ad2ad7
--- /dev/null
+++ b/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java
@@ -0,0 +1,57 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.util;
+
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+public class CycleDetectingMapper<T, R> {
+        private static final String SEPARATOR = " -> ";
+
+        private final Function<T, String> getName;
+
+        private final Function<T, R> doMap;
+
+        private final Set<T> inProgress = new LinkedHashSet<>();
+
+        private final Map<T, R> results = new HashMap<>();
+
+        public CycleDetectingMapper(Function<T, String> getName, Function<T, R> doMap) {
+                this.getName = getName;
+                this.doMap = doMap;
+        }
+
+        public R map(T input) {
+                if (inProgress.contains(input)) {
+                        var path = inProgress.stream().map(getName).collect(Collectors.joining(SEPARATOR));
+                        throw new IllegalArgumentException("Circular reference %s%s%s detected".formatted(path, SEPARATOR,
+                                        getName.apply(input)));
+                }
+                // We can't use computeIfAbsent here, because translating referenced queries calls this method in a reentrant
+                // way, which would cause a ConcurrentModificationException with computeIfAbsent.
+                @SuppressWarnings("squid:S3824")
+                var result = results.get(input);
+                if (result == null) {
+                        inProgress.add(input);
+                        try {
+                                result = doMap.apply(input);
+                                results.put(input, result);
+                        } finally {
+                                inProgress.remove(input);
+                        }
+                }
+                return result;
+        }
+
+        public List<T> getInProgress() {
+                return List.copyOf(inProgress);
+        }
+
+        public R getAlreadyMapped(T input) {
+                return results.get(input);
+        }
+}
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/MapUnitTests.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/MapUnitTests.java
index 6889fd07..2be49bd9 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/MapUnitTests.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/MapUnitTests.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/CommitFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/CommitFuzzTest.java
index 7977f772..58206eda 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/CommitFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/CommitFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import org.junit.jupiter.api.Tag;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/ContentEqualsFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/ContentEqualsFuzzTest.java
index 99e76649..c49911b8 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/ContentEqualsFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/ContentEqualsFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import org.junit.jupiter.api.Tag;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/DiffCursorFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/DiffCursorFuzzTest.java
index e02448cf..5a4f8038 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/DiffCursorFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/DiffCursorFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import org.junit.jupiter.api.Tag;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadFuzzTest.java
index ea58e1b7..3b55434c 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import org.junit.jupiter.api.Tag;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadTestRunnable.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadTestRunnable.java
index f449ca97..9b2e591a 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadTestRunnable.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MultiThreadTestRunnable.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import java.util.ArrayList;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableFuzzTest.java
index 61b17362..fdcd7f9f 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import static org.junit.jupiter.api.Assertions.fail;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableImmutableCompareFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableImmutableCompareFuzzTest.java
index cee15fe1..420dade6 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableImmutableCompareFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/MutableImmutableCompareFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import static org.junit.jupiter.api.Assertions.fail;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/RestoreFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/RestoreFuzzTest.java
index 1661cccb..0b399c3a 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/RestoreFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/RestoreFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import org.junit.jupiter.api.Tag;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/SharedStoreFuzzTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/SharedStoreFuzzTest.java
index 0544687a..680d962d 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/SharedStoreFuzzTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/SharedStoreFuzzTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz;
 
 import java.util.HashMap;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtils.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtils.java
index 89c01690..32675635 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtils.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtils.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz.utils;
 
 import java.util.Arrays;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtilsTest.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtilsTest.java
index 8c641205..951d6336 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtilsTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/fuzz/utils/FuzzTestUtilsTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.fuzz.utils;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/map/tests/utils/MapTestEnvironment.java b/subprojects/store/src/test/java/tools/refinery/store/map/tests/utils/MapTestEnvironment.java
index 0e695aaa..e7348370 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/map/tests/utils/MapTestEnvironment.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/map/tests/utils/MapTestEnvironment.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.map.tests.utils;
 
 import tools.refinery.store.map.*;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/model/hashtests/HashEfficiencyTest.java b/subprojects/store/src/test/java/tools/refinery/store/model/hashtests/HashEfficiencyTest.java
index bb083805..4d4f5e26 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/model/hashtests/HashEfficiencyTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/model/hashtests/HashEfficiencyTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.hashtests;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java b/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
index 371b5e47..56b75804 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/model/tests/ModelTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.model.tests;
 
 import org.junit.jupiter.api.Test;
@@ -9,27 +14,24 @@ import tools.refinery.store.tuple.Tuple;
 import static org.junit.jupiter.api.Assertions.*;
 
 class ModelTest {
+        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
+        private static final Symbol<Integer> age = Symbol.of("age", 1, Integer.class);
+        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
+
         @Test
         void modelConstructionTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, Boolean.class, false);
-
                 var store = ModelStore.builder().symbols(person, friend).build();
                 var symbols = store.getSymbols();
 
                 assertTrue(symbols.contains(person));
                 assertTrue(symbols.contains(friend));
 
-                var other = new Symbol<>("other", 2, Integer.class, null);
+                var other = Symbol.of("other", 2, Integer.class);
                 assertFalse(symbols.contains(other));
         }
 
         @Test
         void modelBuildingTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var age = new Symbol<>("age", 1, Integer.class, null);
-                var friend = new Symbol<>("friend", 2, Boolean.class, false);
-
                 var store = ModelStore.builder().symbols(person, age, friend).build();
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
@@ -49,7 +51,7 @@ class ModelTest {
 
                 assertEquals(3, ageInterpretation.get(Tuple.of(0)));
                 assertEquals(1, ageInterpretation.get(Tuple.of(1)));
-                assertNull(ageInterpretation.get( Tuple.of(2)));
+                assertNull(ageInterpretation.get(Tuple.of(2)));
 
                 assertTrue(friendInterpretation.get(Tuple.of(0, 1)));
                 assertFalse(friendInterpretation.get(Tuple.of(0, 5)));
@@ -57,8 +59,6 @@ class ModelTest {
 
         @Test
         void modelBuildingArityFailTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-
                 var store = ModelStore.builder().symbols(person).build();
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
@@ -70,8 +70,6 @@ class ModelTest {
 
         @Test
         void modelBuildingNullFailTest() {
-                var age = new Symbol<>("age", 1, Integer.class, null);
-
                 var store = ModelStore.builder().symbols(age).build();
                 var model = store.createEmptyModel();
                 var ageInterpretation = model.getInterpretation(age);
@@ -84,10 +82,6 @@ class ModelTest {
 
         @Test
         void modelUpdateTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var age = new Symbol<>("age", 1, Integer.class, null);
-                var friend = new Symbol<>("friend", 2, Boolean.class, false);
-
                 var store = ModelStore.builder().symbols(person, age, friend).build();
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
@@ -113,9 +107,6 @@ class ModelTest {
 
         @Test
         void restoreTest() {
-                var person = new Symbol<>("Person", 1, Boolean.class, false);
-                var friend = new Symbol<>("friend", 2, Boolean.class, false);
-
                 var store = ModelStore.builder().symbols(person, friend).build();
                 var model = store.createEmptyModel();
                 var personInterpretation = model.getInterpretation(person);
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalTest.java
index 96fdc49e..6a66fa84 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.params.ParameterizedTest;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalsTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalsTest.java
index 4a9ef8da..9fe76159 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalsTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/CardinalityIntervalsTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/EmptyCardinalityIntervalTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/EmptyCardinalityIntervalTest.java
index e8b77b9f..24a788a8 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/EmptyCardinalityIntervalTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/EmptyCardinalityIntervalTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteCardinalityIntervalTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteCardinalityIntervalTest.java
index 9a190818..6cf56fae 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteCardinalityIntervalTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteCardinalityIntervalTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinalityTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinalityTest.java
index 90c21759..7c641c47 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinalityTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinalityTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalitiesTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalitiesTest.java
index 3c7c0320..e61f7b36 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalitiesTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalitiesTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.api.Test;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalityTest.java b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalityTest.java
index e87ce29b..10b4dd20 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalityTest.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/representation/cardinality/UpperCardinalityTest.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.representation.cardinality;
 
 import org.junit.jupiter.params.ParameterizedTest;
diff --git a/subprojects/store/src/test/java/tools/refinery/store/util/CollectionsUtilTests.java b/subprojects/store/src/test/java/tools/refinery/store/util/CollectionsUtilTests.java
index 171be0e5..8d50fa8a 100644
--- a/subprojects/store/src/test/java/tools/refinery/store/util/CollectionsUtilTests.java
+++ b/subprojects/store/src/test/java/tools/refinery/store/util/CollectionsUtilTests.java
@@ -1,3 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
 package tools.refinery.store.util;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;