Merge main into qiyuan-inspireretry

- Integrated Sonia's 3.1 task (texkeys extraction and key cleanup)
- Kept retry mechanism and validation from 3.2 task
- Combined both features for complete INSPIRE fetcher improvement
- Removed test documentation file

Author: QiyuanHananu

.github/dependabot.yml

@@ -3,6 +3,7 @@ updates:
   - package-ecosystem: gradle
     directories:
       - "/build-logic"   # versions of 3rd party gradle plugins
+      - "jablib"
       - "/versions"      # versions of 3rd party dependencies of all JabRef modules
       - "/"              # plugins
     schedule:

.github/ghprcomment.yml

@@ -201,11 +201,7 @@
   message: |
     Your pull request needs to link an issue correctly.
 
-    To ease organizational workflows, please link this pull-request to the issue with syntax as described in <https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue>:
-
-    > <h2 id="linking-a-pull-request-to-an-issue-using-a-keyword">Linking a pull request to an issue using a keyword</h2>
-    > <p>You can link a pull request to an issue by using a supported keyword
-    > in the pull request's description or in a commit message.
+    To ease organizational workflows, please link this pull request to the issue by including a supported keyword in the pull request's description as per syntax described in [GitHub's documentation](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue).
 
     ### Examples
 

.github/workflows/binaries.yml

@@ -199,7 +199,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash

.github/workflows/on-issue-labeled.yml

@@ -41,7 +41,7 @@ jobs:
       issues: write
     steps:
     - name: GreetingFirstTimeCodeContribution
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         issue-number: ${{ github.event.issue.number || github.event.pull_request.number }}
         body: |

.github/workflows/pr-comment.yml

@@ -92,7 +92,7 @@ jobs:
       # This step runs in both cases using the proper variables.
       - name: ghprcomment@main
         if: ${{ github.event_name == 'workflow_dispatch' || (steps.check-label.outputs.has_label == 'false' && steps.read-pr_number.outputs.pr_number != '' && steps.isCrossRepository.outputs.isCrossRepository == 'true') }}
-        uses: jbangdev/[email protected].0
+        uses: jbangdev/[email protected].1
         with:
           script: https://github.com/koppor/ghprcomment/blob/main/ghprcomment.java
           scriptargs: "-r JabRef/jabref -p ${{ steps.set-vars.outputs.pr_number }} -w ${{ steps.set-vars.outputs.workflow_run_id }}"

.github/workflows/publish.yml

@@ -96,7 +96,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash

.github/workflows/run-openrewrite.yml

@@ -37,7 +37,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash

.github/workflows/sbom-pr.yml

@@ -27,7 +27,7 @@ jobs:
           cache: 'gradle'
 
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
 
       - name: Generate aggregated CycloneDX SBOM
         run: ./gradlew cyclonedxBom

.github/workflows/tests-code-fetchers.yml

@@ -60,7 +60,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env:

.github/workflows/tests-code.yml

@@ -62,7 +62,7 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -96,7 +96,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -143,7 +143,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -261,7 +261,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -311,7 +311,7 @@ jobs:
       - name: Setup JBang
         uses: jbangdev/setup-jbang@main
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Run ${{ matrix.module }} tests
         run: xvfb-run --auto-servernum ./gradlew :${{ matrix.module }}:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
@@ -346,7 +346,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -396,7 +396,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -463,6 +463,9 @@ jobs:
       - run: jbang build --fresh .jbang/JabKitLauncher.java
       - run: jbang build --fresh .jbang/JabLsLauncher.java
       - run: jbang build --fresh .jbang/JabSrvLauncher.java
+      - run: jbang run .jbang/JabKitLauncher.java --help
+      - run: jbang run .jbang/JabLsLauncher.java --help
+      - run: jbang run .jbang/JabSrvLauncher.java --help
 
   jbang-pr:
     name: JBang (PR)
@@ -499,7 +502,6 @@ jobs:
             jbang-
       - name: Setup JBang
         uses: jbangdev/setup-jbang@main
-
       - name: Detect changed jablib classes
         id: changed-jablib-files
         uses: tj-actions/changed-files@v47
@@ -508,7 +510,6 @@ jobs:
             jablib/src/main/java/**/*.java
           files_ignore: |
             jablib/src/main/java/**/*-*.java
-
       - name: Build ${{ matrix.launcher }} launcher including changed classes
         shell: bash
         # We always run, because changes in jabls, jabsrv also could cause JBang to fail
@@ -518,6 +519,8 @@ jobs:
             echo "//SOURCES ../$f" >> ".jbang/${{ matrix.launcher }}.java"
           done
           jbang build --fresh ".jbang/${{ matrix.launcher }}.java"
+      - run: jbang ".jbang/${{ matrix.launcher }}.java" --help
+        shell: bash
 
   codecoverage:
     if: false
@@ -563,7 +566,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - name: Generate JBang cache key
         id: cache-key
         shell: bash
@@ -609,7 +612,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v4
+        uses: gradle/actions/setup-gradle@v5
       - run: ./gradlew traceRequirements
       - if: always()
         run: cat build/reports/tracing.txt
@@ -623,4 +626,4 @@ jobs:
       - uses: actions/checkout@v5
         with:
           show-progress: 'false'
-      - uses: gradle/actions/wrapper-validation@v4
+      - uses: gradle/actions/wrapper-validation@v5