8 files changed, 111 insertions, 33 deletions

diff --git a/buildSrc/src/main/kotlin/tools/refinery/gradle/java-application.gradle.kts b/buildSrc/src/main/kotlin/tools/refinery/gradle/java-application.gradle.kts
index 68a44f47..469ebf59 100644
--- a/buildSrc/src/main/kotlin/tools/refinery/gradle/java-application.gradle.kts
+++ b/buildSrc/src/main/kotlin/tools/refinery/gradle/java-application.gradle.kts
@@ -12,11 +12,6 @@ plugins {
         id("tools.refinery.gradle.java-conventions")
 }
 
-// Use log4j-over-slf4j instead of log4j 1.x when running the application.
-configurations.runtimeClasspath {
-        exclude(group = "log4j", module = "log4j")
-}
-
 val libs = the<LibrariesForLibs>()
 
 dependencies {
diff --git a/buildSrc/src/main/kotlin/tools/refinery/gradle/java-conventions.gradle.kts b/buildSrc/src/main/kotlin/tools/refinery/gradle/java-conventions.gradle.kts
index db0c87c5..620543a3 100644
--- a/buildSrc/src/main/kotlin/tools/refinery/gradle/java-conventions.gradle.kts
+++ b/buildSrc/src/main/kotlin/tools/refinery/gradle/java-conventions.gradle.kts
@@ -18,26 +18,29 @@ repositories {
         mavenCentral()
 }
 
-// Use log4j-over-slf4j instead of log4j 1.x in the tests.
-configurations.testRuntimeClasspath {
-        exclude(group = "log4j", module = "log4j")
+configurations.withType(Configuration::class) {
+        if (name.endsWith("Classpath")) {
+                exclude(group = "log4j", module = "log4j")
+                exclude(group = "ch.qos.reload4j", module = "reload4j")
+        }
 }
 
 val libs = the<LibrariesForLibs>()
 
 dependencies {
         compileOnly(libs.jetbrainsAnnotations)
+        compileOnly(libs.slf4j.log4j)
         testCompileOnly(libs.jetbrainsAnnotations)
         testImplementation(libs.hamcrest)
         testImplementation(libs.junit.api)
-        testImplementation(enforcedPlatform(libs.junit.bom))
+        testImplementation(enforcedPlatform(project(":refinery-bom-dependencies")))
         testRuntimeOnly(libs.junit.engine)
         testRuntimeOnly(libs.junit.launcher)
+        testRuntimeOnly(libs.slf4j.simple)
         testImplementation(libs.junit.params)
         testImplementation(libs.mockito.core)
         testImplementation(libs.mockito.junit)
-        testImplementation(libs.slf4j.simple)
-        testRuntimeOnly(libs.slf4j.log4j)
+        testImplementation(libs.slf4j.log4j)
 }
 
 java {
diff --git a/buildSrc/src/main/kotlin/tools/refinery/gradle/jmh.gradle.kts b/buildSrc/src/main/kotlin/tools/refinery/gradle/jmh.gradle.kts
index fbbbba11..5dde7033 100644
--- a/buildSrc/src/main/kotlin/tools/refinery/gradle/jmh.gradle.kts
+++ b/buildSrc/src/main/kotlin/tools/refinery/gradle/jmh.gradle.kts
@@ -35,7 +35,10 @@ configurations["jmhRuntimeOnly"].extendsFrom(configurations.runtimeOnly.get(), c
 val libs = the<LibrariesForLibs>()
 
 dependencies {
+        jmhImplementation(enforcedPlatform(project(":refinery-bom-dependencies")))
         jmhImplementation(libs.jmh.core)
+        jmhImplementation(libs.slf4j.log4j)
+        jmhImplementation(libs.slf4j.simple)
         jmhAnnotationProcessor(libs.jmh.annprocess)
 }
 
diff --git a/buildSrc/src/main/kotlin/tools/refinery/gradle/mwe2.gradle.kts b/buildSrc/src/main/kotlin/tools/refinery/gradle/mwe2.gradle.kts
index 91251b45..c20adb85 100644
--- a/buildSrc/src/main/kotlin/tools/refinery/gradle/mwe2.gradle.kts
+++ b/buildSrc/src/main/kotlin/tools/refinery/gradle/mwe2.gradle.kts
@@ -15,15 +15,19 @@ val mwe2: Configuration by configurations.creating {
         isCanBeConsumed = false
         isCanBeResolved = true
         extendsFrom(configurations.implementation.get())
+        // Exclude also here, because the name of this configuration doesn't end with {@code Classpath},
+        // so it isn't caught by {@code tools.refinery.gradle.java-conventions}.
         exclude(group = "log4j", module = "log4j")
+        exclude(group = "ch.qos.reload4j", module = "reload4j")
 }
 
 val libs = the<LibrariesForLibs>()
 
 dependencies {
+        mwe2(enforcedPlatform(project(":refinery-bom-dependencies")))
         mwe2(libs.mwe2.launch)
-        mwe2(libs.slf4j.simple)
         mwe2(libs.slf4j.log4j)
+        mwe2(libs.slf4j.simple)
 }
 
 eclipse.classpath.plusConfigurations += mwe2
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index f57f4597..3ef535e7 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -3,35 +3,99 @@
 # SPDX-License-Identifier: EPL-2.0
 
 [versions]
+antlr = "3.2" # To retain Xtext compatibility, this mustn't be increased
+apiguardian = "1.1.2"
+asm = "9.7"
+classgraph = "4.8.174"
+eclipse-commands = "3.12.100"
+eclipse-contenttype = "3.9.400"
+eclipse-debug = "3.21.400"
+eclipse-filesystem = "1.10.400"
+eclipse-jobs = "3.15.300"
+eclipse-osgi = "3.20.0"
+eclipse-resources = "3.20.200"
+eclipse-runtime = "3.31.100"
+eclipse-text = "3.14.100"
+eclipse-variables = "3.6.400"
 eclipseCollections = "11.1.0"
 ecore = "2.36.0"
-ecoreCodegen = "2.38.0"
-ecoreXmi = "2.37.0"
+ecore-change = "2.16.0"
+ecore-codegen = "2.38.0"
+ecore-xmi = "2.37.0"
+emf-codegen = "2.23.0"
+emf-common = "2.30.0"
+equinox-common = "3.19.100"
+equinox-preferences = "3.11.100"
+equinox-registry = "3.12.100"
+errorprone = "2.28.0"
+findbugs = "3.0.2"
+guava = "33.2.1-jre"
+guice = "7.0.0"
 gson = "2.11.0"
 hamcrest = "2.2"
+jakartaInject = "2.0.1"
 jcommander = "1.83"
+jdt-core = "3.38.0"
+jdt-debug = "3.21.400"
+jdt-launching = "3.22.0"
 jetbrainsAnnotations = "24.1.0"
 jetty = "12.0.11"
 jmh = "1.37"
+jna = "5.14.0"
 junit = "5.10.3"
+lsp4j = "0.23.1"
 mockito = "5.12.0"
 mwe = "1.12.0"
 mwe2 = "2.18.0"
+opentest4j = "1.3.0"
 ortools = "9.10.4067"
-refineryZ3 = "4.12.6"
+protobuf = "4.27.2"
+refinery-z3 = "4.12.6"
 slf4j = "2.0.13"
 xtext = "2.35.0"
-xtextAntlrGenerator = "2.1.1"
+xtext-generator-antlr = "2.1.1"
 
 [libraries]
+antlr = { group = "org.antlr", name = "antlr-runtime", version.ref = "antlr" }
+apiguardian = { group = "org.apiguardian", name = "apiguardian-api", version.ref = "apiguardian" }
+asm = { group = "org.ow2.asm", name = "asm", version.ref = "asm" }
+asm-commons = { group = "org.ow2.asm", name = "asm-commons", version.ref = "asm" }
+asm-tree = { group = "org.ow2.asm", name = "asm-tree", version.ref = "asm" }
+classgraph = { group = "io.github.classgraph", name = "classgraph", version.ref = "classgraph" }
+eclipse-commands = { group = "org.eclipse.platform", name = "org.eclipse.core.commands", version.ref = "eclipse-commands" }
+eclipse-contenttype = { group = "org.eclipse.platform", name = "org.eclipse.core.contenttype", version.ref = "eclipse-contenttype" }
+eclipse-debug = { group = "org.eclipse.platform", name = "org.eclipse.debug.core", version.ref = "eclipse-debug" }
+eclipse-expressions = { group = "org.eclipse.platform", name = "org.eclipse.core.expressions", version.ref = "eclipse-contenttype" }
+eclipse-filesystem = { group = "org.eclipse.platform", name = "org.eclipse.core.filesystem", version.ref = "eclipse-filesystem" }
+eclipse-jobs = { group = "org.eclipse.platform", name = "org.eclipse.core.jobs", version.ref = "eclipse-jobs" }
+eclipse-osgi = { group = "org.eclipse.platform", name = "org.eclipse.osgi", version.ref = "eclipse-osgi" }
+eclipse-resources = { group = "org.eclipse.platform", name = "org.eclipse.core.resources", version.ref = "eclipse-resources" }
+eclipse-runtime = { group = "org.eclipse.platform", name = "org.eclipse.core.runtime", version.ref = "eclipse-runtime" }
+eclipse-text = { group = "org.eclipse.platform", name = "org.eclipse.text", version.ref = "eclipse-text" }
+eclipse-variables = { group = "org.eclipse.platform", name = "org.eclipse.core.variables", version.ref = "eclipse-variables" }
 eclipseCollections = { group = "org.eclipse.collections", name = "eclipse-collections-api", version.ref = "eclipseCollections" }
 eclipseCollections-impl = { group = "org.eclipse.collections", name = "eclipse-collections", version.ref = "eclipseCollections" }
 ecore = { group = "org.eclipse.emf", name = "org.eclipse.emf.ecore", version.ref = "ecore" }
-ecore-codegen = { group = "org.eclipse.emf", name = "org.eclipse.emf.codegen.ecore", version.ref = "ecoreCodegen" }
-ecore-xmi = { group = "org.eclipse.emf", name = "org.eclipse.emf.ecore.xmi", version.ref = "ecoreXmi" }
+ecore-change = { group = "org.eclipse.emf", name = "org.eclipse.emf.ecore.change", version.ref = "ecore-change" }
+ecore-codegen = { group = "org.eclipse.emf", name = "org.eclipse.emf.codegen.ecore", version.ref = "ecore-codegen" }
+ecore-xmi = { group = "org.eclipse.emf", name = "org.eclipse.emf.ecore.xmi", version.ref = "ecore-xmi" }
+emf-codegen = { group = "org.eclipse.emf", name = "org.eclipse.emf.codegen", version.ref = "emf-codegen" }
+emf-common = { group = "org.eclipse.emf", name = "org.eclipse.emf.common", version.ref = "emf-common" }
+equinox-common = { group = "org.eclipse.platform", name = "org.eclipse.equinox.common", version.ref = "equinox-common" }
+equinox-preferences = { group = "org.eclipse.platform", name = "org.eclipse.equinox.preferences", version.ref = "equinox-preferences" }
+equinox-registry = { group = "org.eclipse.platform", name = "org.eclipse.equinox.registry", version.ref = "equinox-registry" }
+errorprone-annotations = { group = "com.google.errorprone", name = "error_prone_annotations", version.ref = "errorprone" }
+findbugs-jsr305 = { group = "com.google.code.findbugs", name = "jsr305", version.ref = "findbugs" }
 gson = { group = "com.google.code.gson", name = "gson", version.ref = "gson" }
+guava = { group = "com.google.guava", name = "guava", version.ref = "guava" }
+guice  = { group = "com.google.inject", name = "guice", version.ref = "guice" }
 hamcrest = { group = "org.hamcrest", name = "hamcrest", version.ref = "hamcrest" }
 jcommander = { group = "org.jcommander", name = "jcommander", version.ref = "jcommander" }
+jdt-core = { group = "org.eclipse.jdt", name = "org.eclipse.jdt.core", version.ref = "jdt-core" }
+jdt-debug = { group = "org.eclipse.jdt", name = "org.eclipse.jdt.debug", version.ref = "jdt-debug" }
+jdt-ecj = { group = "org.eclipse.jdt", name = "ecj", version.ref = "jdt-core" }
+jdt-launching = { group = "org.eclipse.jdt", name = "org.eclipse.jdt.launching", version.ref = "jdt-launching" }
+jakartaInject = { group = "jakarta.inject", name = "jakarta.inject-api", version.ref = "jakartaInject" }
 jetbrainsAnnotations = { group = "org.jetbrains", name = "annotations", version.ref = "jetbrainsAnnotations" }
 jetty-server = { group = "org.eclipse.jetty", name = "jetty-server", version.ref = "jetty" }
 jetty-servlet = { group = "org.eclipse.jetty.ee10", name = "jetty-ee10-servlet", version.ref = "jetty" }
@@ -40,24 +104,33 @@ jetty-websocket-client = { group = "org.eclipse.jetty.websocket", name = "jetty-
 jetty-websocket-server = { group = "org.eclipse.jetty.ee10.websocket", name = "jetty-ee10-websocket-jetty-server", version.ref = "jetty" }
 jmh-core = { group = "org.openjdk.jmh", name = "jmh-core", version.ref = "jmh" }
 jmh-annprocess = { group = "org.openjdk.jmh", name = "jmh-generator-annprocess", version.ref = "jmh" }
+jna = { group = "net.java.dev.jna", name = "jna", version.ref = "jna" }
+jna-platform = { group = "net.java.dev.jna", name = "jna-platform", version.ref = "jna" }
 junit-api = { group = "org.junit.jupiter", name = "junit-jupiter-api" }
 junit-bom = { group = "org.junit", name = "junit-bom", version.ref = "junit" }
 junit-engine = { group = "org.junit.jupiter", name = "junit-jupiter-engine" }
 junit-launcher = { group = "org.junit.platform", name = "junit-platform-launcher" }
 junit-params = { group = "org.junit.jupiter", name = "junit-jupiter-params" }
+lsp4j = { group = "org.eclipse.lsp4j", name = "org.eclipse.lsp4j", version.ref = "lsp4j" }
+lsp4j-jsonrpc = { group = "org.eclipse.lsp4j", name = "org.eclipse.lsp4j.jsonrpc", version.ref = "lsp4j" }
 mockito-core = { group = "org.mockito", name = "mockito-core", version.ref = "mockito" }
 mockito-junit = { group = "org.mockito", name = "mockito-junit-jupiter", version.ref = "mockito" }
+mwe-core = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe.core", version.ref = "mwe" }
 mwe-utils = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe.utils", version.ref = "mwe" }
+mwe2-language = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe2.language", version.ref = "mwe2" }
 mwe2-launch = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe2.launch", version.ref = "mwe2" }
 mwe2-lib = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe2.lib", version.ref = "mwe2" }
+mwe2-runtime = { group = "org.eclipse.emf", name = "org.eclipse.emf.mwe2.runtime", version.ref = "mwe2" }
+opentest4j = { group = "org.opentestj4", name = "opentest4j", version.ref = "opentest4j" }
 ortools = { group = "com.google.ortools", name = "ortools-java", version.ref = "ortools" }
-refinery-z3 = { group = "tools.refinery.z3", name = "refinery-z3-solver", version.ref = "refineryZ3" }
+protobuf = { group = "com.google.protobuf", name = "protobuf-java", version.ref = "protobuf" }
+refinery-z3 = { group = "tools.refinery.z3", name = "refinery-z3-solver", version.ref = "refinery-z3" }
 slf4j = { group = "org.slf4j", name = "slf4j-api", version.ref = "slf4j" }
 slf4j-simple = { group = "org.slf4j", name = "slf4j-simple", version.ref = "slf4j" }
 slf4j-log4j = { group = "org.slf4j", name = "log4j-over-slf4j", version.ref = "slf4j" }
 xtext-core = { group = "org.eclipse.xtext", name = "org.eclipse.xtext", version.ref = "xtext" }
-xtext-generator-antlr = { group = "org.eclipse.xtext", name = "xtext-antlr-generator", version.ref = "xtextAntlrGenerator" }
 xtext-generator = { group = "org.eclipse.xtext", name = "org.eclipse.xtext.xtext.generator", version.ref = "xtext" }
+xtext-generator-antlr = { group = "org.eclipse.xtext", name = "xtext-antlr-generator", version.ref = "xtext-generator-antlr" }
 xtext-ide = { group = "org.eclipse.xtext", name = "org.eclipse.xtext.ide", version.ref = "xtext" }
 xtext-testing = { group = "org.eclipse.xtext", name = "org.eclipse.xtext.testing", version.ref = "xtext" }
 xtext-web = { group = "org.eclipse.xtext", name = "org.eclipse.xtext.web", version.ref = "xtext" }
diff --git a/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/RefineryJavaPlugin.java b/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/RefineryJavaPlugin.java
index 434010d5..4107695e 100644
--- a/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/RefineryJavaPlugin.java
+++ b/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/RefineryJavaPlugin.java
@@ -7,6 +7,7 @@ package tools.refinery.gradle.plugins;
 
 import org.gradle.api.Plugin;
 import org.gradle.api.Project;
+import org.gradle.api.artifacts.Configuration;
 import org.gradle.api.component.AdhocComponentWithVariants;
 import org.gradle.api.component.ConfigurationVariantDetails;
 import org.gradle.api.internal.tasks.JvmConstants;
@@ -24,6 +25,7 @@ import tools.refinery.gradle.plugins.internal.Versions;
 
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
+import java.util.Map;
 
 public class RefineryJavaPlugin implements Plugin<Project> {
         private static final String JUNIT_API = "org.junit.jupiter:junit-jupiter-api";
@@ -97,15 +99,17 @@ public class RefineryJavaPlugin implements Plugin<Project> {
                                         dependencies.enforcedPlatform(artifact) : dependencies.platform(artifact);
                 }));
 
+                RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.COMPILE_ONLY_CONFIGURATION_NAME,
+                                SLF4J_LOG4J, extension.getUseSlf4JLog4J());
                 RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.TEST_IMPLEMENTATION_CONFIGURATION_NAME,
                                 SLF4J_LOG4J, extension.getUseSlf4JLog4J());
                 RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.IMPLEMENTATION_CONFIGURATION_NAME,
                                 SLF4J_LOG4J, extension.getUseSlf4JLog4J().map(value ->
                                                 Boolean.TRUE.equals(value) && target.getPlugins().hasPlugin(ApplicationPlugin.class)));
 
-                RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.TEST_IMPLEMENTATION_CONFIGURATION_NAME,
+                RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.TEST_RUNTIME_ONLY_CONFIGURATION_NAME,
                                 SLF4J_SIMPLE, extension.getUseSlf4JSimple());
-                RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.IMPLEMENTATION_CONFIGURATION_NAME,
+                RefineryPluginUtils.addConditionalDependency(dependencies, JavaPlugin.RUNTIME_ONLY_CONFIGURATION_NAME,
                                 SLF4J_SIMPLE, extension.getUseSlf4JSimple().map(value ->
                                                 Boolean.TRUE.equals(value) && target.getPlugins().hasPlugin(ApplicationPlugin.class)));
 
@@ -197,10 +201,12 @@ public class RefineryJavaPlugin implements Plugin<Project> {
         }
 
         private static void excludeLog4J(Project project) {
-                RefineryPluginUtils.excludeLog4J(project, JavaPlugin.TEST_RUNTIME_CLASSPATH_CONFIGURATION_NAME);
-                if (project.getPlugins().hasPlugin(ApplicationPlugin.class)) {
-                        RefineryPluginUtils.excludeLog4J(project, JavaPlugin.RUNTIME_CLASSPATH_CONFIGURATION_NAME);
-                }
+                project.getConfigurations().withType(Configuration.class, configuration -> {
+                        if (configuration.getName().endsWith("Classpath")) {
+                                configuration.exclude(Map.of("group", "log4j", "module", "log4j"));
+                                configuration.exclude(Map.of("group", "ch.qos.reload4j", "module", "reload4j"));
+                        }
+                });
         }
 
         private static void configureJunitPlatform(Project project) {
diff --git a/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/internal/RefineryPluginUtils.java b/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/internal/RefineryPluginUtils.java
index 35ebdae4..0004f249 100644
--- a/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/internal/RefineryPluginUtils.java
+++ b/subprojects/gradle-plugins/src/main/java/tools/refinery/gradle/plugins/internal/RefineryPluginUtils.java
@@ -12,7 +12,6 @@ import org.gradle.api.artifacts.dsl.DependencyHandler;
 import org.gradle.api.provider.Provider;
 
 import java.util.List;
-import java.util.Map;
 
 public final class RefineryPluginUtils {
         public static final String VERSION_PROPERTY = "tools.refinery.version";
@@ -26,11 +25,6 @@ public final class RefineryPluginUtils {
                 throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly.");
         }
 
-        public static void excludeLog4J(Project project, String configurationName) {
-                var testRuntimeClasspath = project.getConfigurations().getByName(configurationName);
-                testRuntimeClasspath.exclude(Map.of("group", "log4j", "module", "log4j"));
-        }
-
         public static void withShadowPlugin(Project project, Action<? super Project> action) {
                 // Method parameter in Gradle API uses raw type.
                 @SuppressWarnings("rawtypes")
diff --git a/subprojects/versions/build.gradle.kts b/subprojects/versions/build.gradle.kts
index 8137a32d..054158cb 100644
--- a/subprojects/versions/build.gradle.kts
+++ b/subprojects/versions/build.gradle.kts
@@ -17,7 +17,7 @@ mavenArtifact {
 }
 
 val refineryVersion = "refinery"
-val interpreterVersion = "refineryInterpreter"
+val interpreterVersion = "refinery-interpreter"
 val interpreterGroup = property("tools.refinery.interpreter.group").toString()
 val shadowVersion = "shadow"