Merge remote-tracking branch 'upstream/main' into fix-issue-10372

* upstream/main: (334 commits)
  Update CSL styles (JabRef#10734)
  Fix the preview panel showing the wrong entry (an entry that is not selected in the entry table) (JabRef#10728)
  Fix cancelling ignored when generating an entry from id (JabRef#10727)
  Merge split localization string (JabRef#10712)
  Downgrade jfx 21.0.1 to jfx 21
  Bump actions/upload-pages-artifact from 2 to 3 (JabRef#10723)
  Bump actions/deploy-pages from 3 to 4 (JabRef#10722)
  Bump org.glassfish.jersey.core:jersey-server from 3.1.4 to 3.1.5 (JabRef#10720)
  Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (JabRef#10717)
  Bump org.apache.pdfbox:pdfbox from 3.0.0 to 3.0.1 (JabRef#10721)
  Bump org.postgresql:postgresql from 42.6.0 to 42.7.1 (JabRef#10718)
  Bump org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2 (JabRef#10719)
  update snapcraft update bug report template
  Show development information
  Release v5.12
  Release v5.12
  add jspecify
  exclude junit jupiter
  Add external libraries
  Update CSL styles (JabRef#10714)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
#	src/main/java/org/jabref/preferences/GuiPreferences.java
#	src/main/java/org/jabref/preferences/JabRefPreferences.java

.devcontainer/devcontainer.json

@@ -31,9 +31,9 @@
         // Install java.
         // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
         "ghcr.io/devcontainers/features/java:1": {
-            "version": "20.0.2-tem",
+            "version": "21.0.1-librca",
             "installGradle": false,
-            "jdkDistro": "tem"
+            "jdkDistro": "librca"
         }
     }
 }

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.10 (latest release)"
+        - "5.12 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,17 +1,18 @@
 <!-- 
 Describe the changes you have made here: what, why, ... 
-Link issues that are fixed, e.g. "Fixes #333".
-If you fixed a koppor issue, link it, e.g. "Fixes https://github.com/koppor/jabref/issues/47".
-The title of the PR must not reference an issue, because GitHub does not support autolinking there.
+Link the issue that will be closed, e.g., "Closes #333".
+If your PR closes a koppor issue, link it using its URL, e.g., "Closes https://github.com/koppor/jabref/issues/47".
+"Closes" is a keyword GitHub uses to link PRs with issues; do not change it.
+Don't reference an issue in the PR title because GitHub does not support auto-linking there.
 -->
 
+### Mandatory checks
 
 <!-- 
 - Go through the list below. Please don't remove any items.
 - [x] done; [ ] not done / not applicable
 -->
 
-### Mandatory checks
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)

.github/workflows/GreetingFirstTimeCodeContribution.yml → .github/workflows/add-greeting-to-issue.yml

@@ -1,4 +1,4 @@
-name: GreetingFirstTimeCodeContribution
+name: Add greeting to issues for first time contributors
 
 on: 
   issues:

.github/workflows/add-to-projects.yml

@@ -0,0 +1,42 @@
+name: Add to Project on Label
+
+on:
+  issues:
+    types: [labeled]
+
+permissions:
+  issues: write
+
+jobs:
+  add-to-project:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: "good first issue"
+        if: "${{ github.event.label.name == 'good first issue' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 5 --owner jabref --url $ISSUE_URL
+      - name: needs-refinement
+        if: github.event.label.name == 'needs-refinement'
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 15 --owner jabref --url $ISSUE_URL
+      - name: "status: freeze"
+        if: "${{ github.event.label.name == 'status: freeze' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 9 --owner jabref --url $ISSUE_URL
+      - name: ui
+        if: "${{ github.event.label.name == 'ui' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 8 --owner jabref --url $ISSUE_URL

.github/workflows/automerge.yml

@@ -10,18 +10,24 @@ jobs:
     runs-on: ubuntu-latest
     # Run only if PR is inside JabRef's main repository and created by dependabot or by an update workflow
     if: >
-      (github.repository == 'JabRef/jabref') &&
-      ((github.actor == 'dependabot[bot]') ||
-       ((startsWith(github.event.pull_request.title, '[Bot] ') || (startsWith(github.event.pull_request.title, 'Bump '))) &&
-       (github.event.pull_request.head.repo.full_name == 'JabRef/jabref')))
+      (github.repository == 'JabRef/jabref') && 
+      (github.event.pull_request.head.repo.full_name == 'JabRef/jabref') &&
+      (
+        (github.actor == 'dependabot[bot]') ||
+        (
+          startsWith(github.event.pull_request.title, '[Bot] ') || 
+          startsWith(github.event.pull_request.title, 'Bump ') || 
+          startsWith(github.event.pull_request.title, 'New Crowdin updates')
+        )
+      )
     steps:
       - name: Approve PR
         run: gh pr review --approve "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
           GITHUB_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
       - name: Merge PR
-        run: gh pr merge --auto "$PR_URL"
+        run: gh pr merge --auto --squash "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}

.github/workflows/check-links.yml

@@ -0,0 +1,35 @@
+name: Check external href links in the documentation
+
+on:
+  push:
+    paths:
+      - '.github/workflows/check-links.yml'
+      - '**/*.md'
+  schedule:
+    # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
+    - cron: "0 9 1 * *"
+  workflow_dispatch:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  lychee:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Restore lychee cache
+        uses: actions/cache@v3
+        with:
+          path: .lycheecache
+          key: cache-lychee-${{ github.sha }}
+          restore-keys: cache-lychee-
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1.8.0
+        with:
+          fail: true
+          args: --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/cleanup_pr.yml → .github/workflows/cleanup-pr.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel deployment run
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.0
         with:
           ignore_sha: true
           workflow_id: 9813 # workflow "Deployment"

.github/workflows/deployment-arm64.yml

@@ -22,7 +22,7 @@ env:
   JAVA_OPTS: -Xmx4g
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -59,25 +59,10 @@ jobs:
         id: gitversion
         uses: gittools/actions/gitversion/execute@v0.10.2
       - name: Setup JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
-          java-version: 20
-          distribution: 'temurin'
-          cache: 'gradle'
-      - name: Setup JDK jabref-fix macOS
-        shell: bash
-        run: |
-            mkdir ${{runner.temp}}/jdk
-            wget -qO- https://files.jabref.org/jdks/jdk-macos-aarch64.tar.gz | tar xz -C ${{runner.temp}}/jdk
-            mv ${{runner.temp}}/jdk/jdk-21.jdk ${{runner.temp}}/jdk/jdk-21
-            echo "JDK21=${{runner.temp}}/jdk/jdk-21" >> "$GITHUB_ENV"
-            ls ${{runner.temp}}/jdk
-
-            echo "org.gradle.java.installations.paths=${{runner.temp}}/jdk/jdk-21" >> gradle.properties
-            echo "org.gradle.java.installations.auto-detect=false" >> gradle.properties
-            cat gradle.properties
-
-            sed -i'.bak' -e "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
+          java-version: 21.0.1
+          distribution: 'liberica'
       - name: Clean up keychain
         run: |
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
@@ -99,14 +84,16 @@ jobs:
           mkdir ${{runner.temp}}/keychain
           security create-keychain -p jabref ${{runner.temp}}/keychain/notarization.keychain
           security set-keychain-settings ${{runner.temp}}/keychain/notarization.keychain
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Build dmg (macOS)
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \
@@ -128,9 +115,9 @@ jobs:
       - name: Build pkg (macOS)
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \
@@ -175,7 +162,7 @@ jobs:
           rsync -Pavz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i ~/.ssh/id_rsa' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store
         if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution