chore(deps): bump dependencies

Also make sure Sonar can process TypeScript files.

7 files changed, 208 insertions, 203 deletions

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 953e67f7..eecb62c1 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -71,7 +71,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed by Sonar to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
-          ./gradlew build sonarqube -Pci --info
+          ./gradlew build sonar -Pci --info
   reuse-check:
     name: REUSE Compliance Check
     runs-on: ubuntu-latest
diff --git a/gradle.properties b/gradle.properties
index d6faa150..d9866f95 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: EPL-2.0
 
 file.encoding=UTF-8
-frontend.nodeVersion=18.15.0
+frontend.nodeVersion=18.16.0
 frontend.yarnVersion=4.0.0-rc.42
 frontend.yarn1Version=1.22.19
 group=tools.refinery
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index 113bf3a5..5cdb0c6e 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -7,13 +7,13 @@ eclipseCollections = "12.0.0.M1"
 jetty = "12.0.0.beta0"
 jmh = "1.36"
 junit = "5.9.2"
-mockito = "5.2.0"
+mockito = "5.3.0"
 mwe2 = "2.14.0"
 slf4j = "2.0.7"
 xtext = "2.31.0.M0"
 
 [libraries]
-jetbrainsAnnotations = { group = "org.jetbrains", name = "annotations", version = "24.0.1"}
+jetbrainsAnnotations = { group = "org.jetbrains", name = "annotations", version = "24.0.1" }
 eclipseCollections = { group = "org.eclipse.collections", name = "eclipse-collections", version.ref = "eclipseCollections" }
 eclipseCollections-api = { group = "org.eclipse.collections", name = "eclipse-collections-api", version.ref = "eclipseCollections" }
 ecore = { group = "org.eclipse.emf", name = "org.eclipse.emf.ecore", version = "2.33.0" }
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index bdc9a83b..0c85a1f7 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.0.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.1-bin.zip
 networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/subprojects/frontend/package.json b/subprojects/frontend/package.json
index cd96a574..655d7260 100644
--- a/subprojects/frontend/package.json
+++ b/subprojects/frontend/package.json
@@ -28,13 +28,13 @@
   },
   "homepage": "https://refinery.tools",
   "dependencies": {
-    "@codemirror/autocomplete": "^6.4.2",
+    "@codemirror/autocomplete": "^6.5.1",
     "@codemirror/commands": "^6.2.2",
     "@codemirror/language": "^6.6.0",
-    "@codemirror/lint": "^6.2.0",
+    "@codemirror/lint": "^6.2.1",
     "@codemirror/search": "^6.3.0",
     "@codemirror/state": "^6.2.0",
-    "@codemirror/view": "^6.9.3",
+    "@codemirror/view": "^6.9.4",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@fontsource/inter": "^4.5.15",
@@ -44,8 +44,8 @@
     "@lezer/lr": "^1.3.3",
     "@material-icons/svg": "^1.0.33",
     "@mui/icons-material": "5.11.16",
-    "@mui/material": "5.11.16",
-    "@vitejs/plugin-react-swc": "^3.2.0",
+    "@mui/material": "5.12.0",
+    "@vitejs/plugin-react-swc": "^3.3.0",
     "ansi-styles": "^6.2.1",
     "csstype": "^3.1.2",
     "escape-string-regexp": "^5.0.0",
@@ -71,10 +71,10 @@
     "@types/ms": "^0.7.31",
     "@types/node": "^18.15.11",
     "@types/prettier": "^2.7.2",
-    "@types/react": "^18.0.33",
+    "@types/react": "^18.0.35",
     "@types/react-dom": "^18.0.11",
-    "@typescript-eslint/eslint-plugin": "^5.57.1",
-    "@typescript-eslint/parser": "^5.57.1",
+    "@typescript-eslint/eslint-plugin": "^5.58.0",
+    "@typescript-eslint/parser": "^5.58.0",
     "@xstate/cli": "^0.4.2",
     "cross-env": "^7.0.3",
     "eslint": "^8.38.0",
@@ -88,7 +88,7 @@
     "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": "^2.8.7",
     "typescript": "5.0.4",
diff --git a/subprojects/frontend/tsconfig.base.json b/subprojects/frontend/tsconfig.base.json
index 58a2a6f2..5ef50b5e 100644
--- a/subprojects/frontend/tsconfig.base.json
+++ b/subprojects/frontend/tsconfig.base.json
@@ -23,7 +23,7 @@
     "noUnusedParameters": true,
     // "verbatimModuleSyntax" is incompatible with `import` syntax in modules
     // with CommonJS import resolution, so we use "isolatedModules" only.
-    "verbatimModuleSyntax": false,
+    // "verbatimModuleSyntax": false,
     "isolatedModules": true,
     "checkJs": true,
     "esModuleInterop": true,
diff --git a/yarn.lock b/yarn.lock
index d2aa900f..292d2fb1 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1273,9 +1273,9 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@codemirror/autocomplete@npm:^6.4.2":
-  version: 6.4.2
-  resolution: "@codemirror/autocomplete@npm:6.4.2"
+"@codemirror/autocomplete@npm:^6.5.1":
+  version: 6.5.1
+  resolution: "@codemirror/autocomplete@npm:6.5.1"
   dependencies:
     "@codemirror/language": "npm:^6.0.0"
     "@codemirror/state": "npm:^6.0.0"
@@ -1286,7 +1286,7 @@ __metadata:
     "@codemirror/state": ^6.0.0
     "@codemirror/view": ^6.0.0
     "@lezer/common": ^1.0.0
-  checksum: d87cb8f208a1c11877522caf93cc6528aff156d52c0ca43833c7789017fe9664c91c39790d4217e9c6ac822b3b523319ccd971ca951b389edd07d526ce70ef02
+  checksum: c5795b5b213ef12cc4671292eab92b8fb5650df5d0b5fbd9c29d3a11e08942cc6c43a639915ed6bb0cd65f2851b4b031e83257faefdb967eaf2df88b76702202
   languageName: node
   linkType: hard
 
@@ -1316,14 +1316,14 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@codemirror/lint@npm:^6.2.0":
-  version: 6.2.0
-  resolution: "@codemirror/lint@npm:6.2.0"
+"@codemirror/lint@npm:^6.2.1":
+  version: 6.2.1
+  resolution: "@codemirror/lint@npm:6.2.1"
   dependencies:
     "@codemirror/state": "npm:^6.0.0"
     "@codemirror/view": "npm:^6.0.0"
     crelt: "npm:^1.0.5"
-  checksum: 638e4b55a477580225e0f97045769891182756a5d74909b2a264dd8ca96d755d7687df88514f7c61abf17bf2ae6c2af927e18c6850169e9ae404489366f277b2
+  checksum: 91293dbac5a7a787fd7ac5ef5227717856f8bc7d9ab0c65b62e112ff0251eb1866d93a78d157599698146b40b7c21028c221f9875af272e6f3bf4dd94cc50247
   languageName: node
   linkType: hard
 
@@ -1345,14 +1345,14 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@codemirror/view@npm:^6.0.0, @codemirror/view@npm:^6.6.0, @codemirror/view@npm:^6.9.3":
-  version: 6.9.3
-  resolution: "@codemirror/view@npm:6.9.3"
+"@codemirror/view@npm:^6.0.0, @codemirror/view@npm:^6.6.0, @codemirror/view@npm:^6.9.4":
+  version: 6.9.4
+  resolution: "@codemirror/view@npm:6.9.4"
   dependencies:
     "@codemirror/state": "npm:^6.1.4"
     style-mod: "npm:^4.0.0"
     w3c-keyname: "npm:^2.2.4"
-  checksum: ab856cd03a87f4a045965ddb1cd051e2120898348593dafa8bd216e79d18f4b6250c463bb35b7ba4d235cfd319a54deecdc54d944e7830337a0145f5e1a21229
+  checksum: 3d00e1c38bb8ea894f2f0928a33036e4095b8e726478001adad07d42b5f0437f051ce5ea5267841a97f262cd21393ecba8f5908acaacd3260f97afbe3a01eb55
   languageName: node
   linkType: hard
 
@@ -1375,16 +1375,16 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@emotion/cache@npm:^11.10.5":
-  version: 11.10.5
-  resolution: "@emotion/cache@npm:11.10.5"
+"@emotion/cache@npm:^11.10.5, @emotion/cache@npm:^11.10.7":
+  version: 11.10.7
+  resolution: "@emotion/cache@npm:11.10.7"
   dependencies:
     "@emotion/memoize": "npm:^0.8.0"
     "@emotion/sheet": "npm:^1.2.1"
     "@emotion/utils": "npm:^1.2.0"
     "@emotion/weak-memoize": "npm:^0.3.0"
     stylis: "npm:4.1.3"
-  checksum: 40c744c5eea3d4438186ea4be71bf691cf3ac16774bda3d6d825960286fa35d735492ae881c028e01881101890f79568107877faefa58d027c760a4207ebe738
+  checksum: c5a4099e8c5bb49c4091747f7284bc10f686d9cf9ceec4088109d4d95d6cf677b1a951a341342a6e8c277300762a3e8aefb3afb45aa9c9c03a1b62b56ac4b2e5
   languageName: node
   linkType: hard
 
@@ -1850,14 +1850,14 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@mui/base@npm:5.0.0-alpha.124":
-  version: 5.0.0-alpha.124
-  resolution: "@mui/base@npm:5.0.0-alpha.124"
+"@mui/base@npm:5.0.0-alpha.125":
+  version: 5.0.0-alpha.125
+  resolution: "@mui/base@npm:5.0.0-alpha.125"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
     "@emotion/is-prop-valid": "npm:^1.2.0"
-    "@mui/types": "npm:^7.2.3"
-    "@mui/utils": "npm:^5.11.13"
+    "@mui/types": "npm:^7.2.4"
+    "@mui/utils": "npm:^5.12.0"
     "@popperjs/core": "npm:^2.11.7"
     clsx: "npm:^1.2.1"
     prop-types: "npm:^15.8.1"
@@ -1869,14 +1869,14 @@ __metadata:
   peerDependenciesMeta:
     "@types/react":
       optional: true
-  checksum: b53460ea251e96d4e976b5167a418c49b4f06e64fff3de620bb7e2b9d8f4a3958e4b0ca92b4173f8f137a8d2f16a6cbbade77ea3cae6ace927bad6ce1a539685
+  checksum: b74d1bec371b85f28bdbb760d08cb783ad10631e2cd2856c9f51c07da67a3d8d830efd246376648595af510da933fba9d9f1e73986df556536036b0c1fc46944
   languageName: node
   linkType: hard
 
-"@mui/core-downloads-tracker@npm:^5.11.16":
-  version: 5.11.16
-  resolution: "@mui/core-downloads-tracker@npm:5.11.16"
-  checksum: a304a45302e64470d73fe07771287203a1f76555085a210e9edb5a5a9af2bc733893d5c26cd0a2cde55c6da084e921c307f0456de6ff47db3927727c49240673
+"@mui/core-downloads-tracker@npm:^5.12.0":
+  version: 5.12.0
+  resolution: "@mui/core-downloads-tracker@npm:5.12.0"
+  checksum: 977a5e9ec1a72224a61e7e56cff15602f0f34afe6384cbae1940a57b699771981360d998d7674217532f713480020a7108abd33c0bd1eaa202e9d828aafa783d
   languageName: node
   linkType: hard
 
@@ -1896,16 +1896,16 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@mui/material@npm:5.11.16":
-  version: 5.11.16
-  resolution: "@mui/material@npm:5.11.16"
+"@mui/material@npm:5.12.0":
+  version: 5.12.0
+  resolution: "@mui/material@npm:5.12.0"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
-    "@mui/base": "npm:5.0.0-alpha.124"
-    "@mui/core-downloads-tracker": "npm:^5.11.16"
-    "@mui/system": "npm:^5.11.16"
-    "@mui/types": "npm:^7.2.3"
-    "@mui/utils": "npm:^5.11.13"
+    "@mui/base": "npm:5.0.0-alpha.125"
+    "@mui/core-downloads-tracker": "npm:^5.12.0"
+    "@mui/system": "npm:^5.12.0"
+    "@mui/types": "npm:^7.2.4"
+    "@mui/utils": "npm:^5.12.0"
     "@types/react-transition-group": "npm:^4.4.5"
     clsx: "npm:^1.2.1"
     csstype: "npm:^3.1.2"
@@ -1925,16 +1925,16 @@ __metadata:
       optional: true
     "@types/react":
       optional: true
-  checksum: 95ab2e550de10673575c219be28a6d2259eac118286e53938582fcd01485ee16c086b96239d0427bd247b464efeaf0fa7805e9da1838ec83be7023428c26b1d1
+  checksum: 5eab5b821b3fc8e98b63d813b275b28f9f26b5cee5e4618bf4414120769483bba987c7fd66d1e2f71ba145630dc329d50e8fed64bd5bbccbccfe6462353666f5
   languageName: node
   linkType: hard
 
-"@mui/private-theming@npm:^5.11.13":
-  version: 5.11.13
-  resolution: "@mui/private-theming@npm:5.11.13"
+"@mui/private-theming@npm:^5.12.0":
+  version: 5.12.0
+  resolution: "@mui/private-theming@npm:5.12.0"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
-    "@mui/utils": "npm:^5.11.13"
+    "@mui/utils": "npm:^5.12.0"
     prop-types: "npm:^15.8.1"
   peerDependencies:
     "@types/react": ^17.0.0 || ^18.0.0
@@ -1942,16 +1942,16 @@ __metadata:
   peerDependenciesMeta:
     "@types/react":
       optional: true
-  checksum: 9028e6be77b517dc4bf902daa4e966441ea982b0c19731028de459272132cfb824c71e8daddb96d2d2c79ed95eb680a322fb1621f464a458e1e04a143bd315c5
+  checksum: 2592d913ce83b52bfc3deb893490f20b9359b28e3e90e800f6cdffb50e050fd7e452892f45f0839506a882b76a0e392bc73c47697e442133a6206cc79f15ace4
   languageName: node
   linkType: hard
 
-"@mui/styled-engine@npm:^5.11.16":
-  version: 5.11.16
-  resolution: "@mui/styled-engine@npm:5.11.16"
+"@mui/styled-engine@npm:^5.12.0":
+  version: 5.12.0
+  resolution: "@mui/styled-engine@npm:5.12.0"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
-    "@emotion/cache": "npm:^11.10.5"
+    "@emotion/cache": "npm:^11.10.7"
     csstype: "npm:^3.1.2"
     prop-types: "npm:^15.8.1"
   peerDependencies:
@@ -1963,19 +1963,19 @@ __metadata:
       optional: true
     "@emotion/styled":
       optional: true
-  checksum: d28876c2752ce3b76efe3ac2c167c59e4fcdcc8fc0aae6374870db258e68c0f9db346c250116391268b89d0d4123e989664c4c32afefd2e45249514edffd6f2c
+  checksum: 6598317424a3791f419bf47e40c60af6e6f2fe7ce7706fe33d10294af8856fd56a96485f0daa5bf0a9da495be7f32c8c54e82efbe33f6eabf55da1bf01623071
   languageName: node
   linkType: hard
 
-"@mui/system@npm:^5.11.16":
-  version: 5.11.16
-  resolution: "@mui/system@npm:5.11.16"
+"@mui/system@npm:^5.12.0":
+  version: 5.12.0
+  resolution: "@mui/system@npm:5.12.0"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
-    "@mui/private-theming": "npm:^5.11.13"
-    "@mui/styled-engine": "npm:^5.11.16"
-    "@mui/types": "npm:^7.2.3"
-    "@mui/utils": "npm:^5.11.13"
+    "@mui/private-theming": "npm:^5.12.0"
+    "@mui/styled-engine": "npm:^5.12.0"
+    "@mui/types": "npm:^7.2.4"
+    "@mui/utils": "npm:^5.12.0"
     clsx: "npm:^1.2.1"
     csstype: "npm:^3.1.2"
     prop-types: "npm:^15.8.1"
@@ -1991,25 +1991,25 @@ __metadata:
       optional: true
     "@types/react":
       optional: true
-  checksum: 3edb017c917c6aac490ae4124a157862f56ad28e1a0f8fc4e78ae81ba42607e4caa1e650aea46d84e1f293bf93b3d8bb435ee6897a087a07ce4e0798457034e8
+  checksum: a2a615875da63a9a52c13b2a454aca08c98b8f131e71ee1170eb8556bb0fc24bed3eb485c9c450aeedaa972f41591fca6b06446af3994640be6dcff20cf5090d
   languageName: node
   linkType: hard
 
-"@mui/types@npm:^7.2.3":
-  version: 7.2.3
-  resolution: "@mui/types@npm:7.2.3"
+"@mui/types@npm:^7.2.4":
+  version: 7.2.4
+  resolution: "@mui/types@npm:7.2.4"
   peerDependencies:
     "@types/react": "*"
   peerDependenciesMeta:
     "@types/react":
       optional: true
-  checksum: f5b074ecdfda55bae66a344e1fd1247920c18ee4548589528643a460de2c9409f6d9ff8ab59c5efa4ff7513d5d83c7a7240613e7e5f36ec71139a0da262cb237
+  checksum: 651ad27d90e052ede4698bea349728bfdd4c415aebcf718e4fb401a281956a33c1748743fe70e5664e75585db94555077658ccf33e6a194b7ee26e44d8e6da8e
   languageName: node
   linkType: hard
 
-"@mui/utils@npm:^5.11.13":
-  version: 5.11.13
-  resolution: "@mui/utils@npm:5.11.13"
+"@mui/utils@npm:^5.12.0":
+  version: 5.12.0
+  resolution: "@mui/utils@npm:5.12.0"
   dependencies:
     "@babel/runtime": "npm:^7.21.0"
     "@types/prop-types": "npm:^15.7.5"
@@ -2018,7 +2018,7 @@ __metadata:
     react-is: "npm:^18.2.0"
   peerDependencies:
     react: ^17.0.0 || ^18.0.0
-  checksum: 8ca3debcb4a506e8b97bde4cfcd7e7358ba5e3b90bc375e36175b623212f509a10caf58621b84de1991a6304b695a7041adbc54cac923d4be19b52f15ef4fff9
+  checksum: dfe539635fddfb14ac77e71c46bde0b73ac893928b85e14ca4987f604ef65ee50529dc0c8ad6ec99da510bfa25ff3e11435b3f9bae122aae2e96675a7e7e1a0b
   languageName: node
   linkType: hard
 
@@ -2094,13 +2094,13 @@ __metadata:
   version: 0.0.0-use.local
   resolution: "@refinery/frontend@workspace:subprojects/frontend"
   dependencies:
-    "@codemirror/autocomplete": "npm:^6.4.2"
+    "@codemirror/autocomplete": "npm:^6.5.1"
     "@codemirror/commands": "npm:^6.2.2"
     "@codemirror/language": "npm:^6.6.0"
-    "@codemirror/lint": "npm:^6.2.0"
+    "@codemirror/lint": "npm:^6.2.1"
     "@codemirror/search": "npm:^6.3.0"
     "@codemirror/state": "npm:^6.2.0"
-    "@codemirror/view": "npm:^6.9.3"
+    "@codemirror/view": "npm:^6.9.4"
     "@emotion/react": "npm:^11.10.6"
     "@emotion/styled": "npm:^11.10.6"
     "@fontsource/inter": "npm:^4.5.15"
@@ -2111,7 +2111,7 @@ __metadata:
     "@lezer/lr": "npm:^1.3.3"
     "@material-icons/svg": "npm:^1.0.33"
     "@mui/icons-material": "npm:5.11.16"
-    "@mui/material": "npm:5.11.16"
+    "@mui/material": "npm:5.12.0"
     "@types/eslint": "npm:^8.37.0"
     "@types/html-minifier-terser": "npm:^7.0.0"
     "@types/lodash-es": "npm:^4.17.7"
@@ -2119,11 +2119,11 @@ __metadata:
     "@types/ms": "npm:^0.7.31"
     "@types/node": "npm:^18.15.11"
     "@types/prettier": "npm:^2.7.2"
-    "@types/react": "npm:^18.0.33"
+    "@types/react": "npm:^18.0.35"
     "@types/react-dom": "npm:^18.0.11"
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 "common-tags@npm:^1.8.0":
   version: 1.8.2
   resolution: "common-tags@npm:1.8.2"
@@ -4687,20 +4692,20 @@ __metadata:
   languageName: node
   linkType: hard
 
-"html-minifier-terser@npm:^7.1.0":
-  version: 7.1.0
-  resolution: "html-minifier-terser@npm:7.1.0"
+"html-minifier-terser@npm:^7.2.0":
+  version: 7.2.0
+  resolution: "html-minifier-terser@npm:7.2.0"
   dependencies:
     camel-case: "npm:^4.1.2"
-    clean-css: "npm:5.2.0"
-    commander: "npm:^9.4.1"
+    clean-css: "npm:~5.3.2"
+    commander: "npm:^10.0.0"
     entities: "npm:^4.4.0"
     param-case: "npm:^3.0.4"
     relateurl: "npm:^0.2.7"
     terser: "npm:^5.15.1"
   bin:
     html-minifier-terser: cli.js
-  checksum: 188f77b3cf44c7d13a6137d3a337c41fa0ac628b4c69816ca4cf4aa60d80eb7803082ddb7d4fd883e386c420bf9cc59c58b8f528c26d9ce0f7adf072edcf8920
+  checksum: 9287823ef09537f522a138930bce6cf28fad9740c194f13dce0b80d22c7870de3814e3e6780f56a4e0bdc2cb20b87af2edbfd12835e3773e60f887bff9e1798f
   languageName: node
   linkType: hard