Merge remote-tracking branch 'upstream/main' into jackson3

* upstream/main: (30 commits)
  Chore(deps): Bump io.github.classgraph:classgraph from 4.8.181 to 4.8.184 in /versions (#14304)
  Chore(deps): Bump com.fasterxml:aalto-xml in /versions (#14311)
  Chore(deps): Bump commons-io:commons-io in /versions (#14310)
  Chore(deps): Bump org.apache.maven.plugins:maven-surefire-plugin (#14298)
  Disable fetcher-gui-test (#14308)
  Chore(deps): Bump com.dlsc.gemsfx:gemsfx in /versions (#14307)
  No labels for dependeabot updates
  Fix fallback window height from 786 to 768 (#14295)
  Chore(deps): Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (#14306)
  Chore(deps): Bump org.apache.maven.plugins:maven-compiler-plugin (#14302)
  Chore(deps): Bump org.apache.maven.plugins:maven-deploy-plugin (#14300)
  Chore(deps): Bump org.apache.maven.plugins:maven-clean-plugin (#14299)
  Chore(deps): Bump jablib/src/main/resources/csl-styles (#14296)
  Chore(deps): Bump com.vanniktech.maven.publish in /jablib (#14303)
  Chore(deps): Bump org.apache.maven.plugins:maven-project-info-reports-plugin (#14297)
  Update all dependencies (#14301)
  Prepare maven3 example project (#14294)
  Refactor StringUtilTest to use parameterized tests (#14126)
  Try to fix download of pr_number
  Fix workflow names
  ...

Author: Siedlerchr

.github/dependabot.yml

@@ -9,8 +9,7 @@ updates:
     schedule:
       interval: weekly
       day: sunday
-    labels:
-      - "dependencies"
+    labels: [ ]
     ignore:
       - dependency-name: com.microsoft.azure:applicationinsights-core
         versions:
@@ -23,10 +22,17 @@ updates:
     schedule:
       interval: weekly
       day: sunday
-    labels:
-      - "dependencies"
+    labels: [ ]
   - package-ecosystem: "gitsubmodule"
     directory: "/"
     schedule:
       interval: weekly
       day: sunday
+    labels: [ ]
+  - package-ecosystem: "maven"
+    directories:
+      - "jablib-examples/maven3/doi-to-bibtex"
+    schedule:
+      interval: weekly
+      day: sunday
+    labels: [ ]

.github/ghprcomment.yml

@@ -179,19 +179,19 @@
     Give it a read, and you’ll discover the ancient wisdom of assigning issues to yourself. Trust me, it’s worth it. 🚀
 
 - jobName: 'PR title must not contain "issue <number>"'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     The title of the pull request must not start with "Fix for issue xyz".
     Please use a concise one-line summary that explains what the fix or change actually does.
     Example of a good title: "Prevent crash when importing malformed BibTeX entries".
 - jobName: 'Mandatory Checks present'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     You have removed the "Mandatory Checks" section from your pull request description. Please adhere to our [pull request template](https://github.com/JabRef/jabref/blob/main/.github/PULL_REQUEST_TEMPLATE.md?plain=1#L10).
 - jobName: 'PR checklist OK'
-  workflowName: 'PR Format'
+  workflowName: 'Check PR Format'
   always: true
   message: >
     Note that your PR will not be reviewed/accepted until you have gone through the mandatory checks in the description and marked each of them them exactly in the format of `[x]` (done), `[ ]` (not done yet) or `[/]` (not applicable).

.github/workflows/on-pr-changes-requested-move-labels.yml

@@ -10,9 +10,9 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     permissions:
-      issues: write
       actions: read
       contents: read
+      pull-requests: write
     steps:
       - name: Download artifact from triggering run
         uses: actions/download-artifact@v6

.github/workflows/on-pr-opened-updated.yml renamed to .github/workflows/on-pr-opened-updated-check.yml

@@ -1,4 +1,4 @@
-name: On PR opened/updated
+name: On PR opened/updated (Check)
 
 on:
   # _target is required
@@ -10,6 +10,9 @@ jobs:
     if: github.repository == 'JabRef/jabref'
     name: Conflicts with target branch
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      actions: write
     steps:
       - uses: actions/checkout@v5
         with:

.github/workflows/on-pr-opened-updated-move-labels.yml

@@ -2,23 +2,24 @@ name: On PR opened/updated (Labels)
 
 on:
   workflow_run:
-    workflows: ["On PR opened/updated"]
+    workflows: ["On PR opened/updated (Check)"]
     types: [completed]
 
 jobs:
    apply-labels:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     permissions:
-      issues: write
       actions: read
       contents: read
+      pull-requests: write
     steps:
       - name: Download artifact from triggering run
         uses: actions/download-artifact@v6
         with:
-          run-id: ${{ github.event.workflow_run.id }}
-          name: pr_number
+            name: pr_number
+            github-token: ${{ secrets.GITHUB_TOKEN }}
+            run-id: ${{ github.event.workflow_run.id }}
         continue-on-error: true
       - name: Check for pr_number.txt
         id: check

.github/workflows/tests-code.yml

@@ -434,7 +434,7 @@ jobs:
       KOPPOR_MAVENCENTRALUSERNAME: ${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
       KOPPOR_MAVENCENTRALPASSWORD: ${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}
 
-  jbang:
+  jbang-main:
     name: JBang (main)
     runs-on: ubuntu-latest
     needs: publish
@@ -452,7 +452,7 @@ jobs:
           files: |
             .jbang/*.java
             jablib/src/main/java/**/*.java
-            jablib-examples/**/*.java
+            jablib-examples/jbang/**/*.java
           files_ignore: |
             jablib/src/main/java/**/*-*.java
       - name: Set up JDK
@@ -488,7 +488,7 @@ jobs:
           done
         if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: |
-          for f in jablib-examples/*.java; do
+          for f in jablib-examples/jbang/*.java; do
             echo "Building $f..."
             jbang build --fresh "$f"
           done
@@ -510,7 +510,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        script: [.jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/ieee_pdf_references_to_bibtex.java]
+        script: [.jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/jbang/doi_to_bibtex.java, jablib-examples/jbang/ieee_pdf_references_to_bibtex.java]
     steps:
       - name: Checkout source
         uses: actions/checkout@v5
@@ -525,7 +525,7 @@ jobs:
             .jbang/*.java
             jabkit/src/main/java/**/*.java
             jablib/src/main/java/**/*.java
-            jablib-examples/**/*.java
+            jablib-examples/jbang/**/*.java
           files_ignore: |
             jablib/src/main/java/**/*-*.java
       - name: Set up JDK
@@ -579,6 +579,60 @@ jobs:
         if: ${{ contains(matrix.script, 'Launcher.java') }}
         shell: bash
 
+  maven-examples:
+    name: Maven examples (main)
+    runs-on: ubuntu-latest
+    needs: publish
+    if: github.ref == 'refs/heads/main'
+    strategy:
+      fail-fast: false
+      matrix:
+        project: [jablib-examples/maven3/doi-to-bibtex]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+        with:
+          submodules: 'false'
+          show-progress: 'false'
+      - name: Set up JDK
+        uses: actions/setup-java@v5
+        with:
+          java-version: 24
+          distribution: 'corretto'
+          cache: maven
+          check-latest: true
+      - run: |
+          cd ${{ matrix.project }}
+          mvn --batch-mode --update-snapshots verify
+        shell: bash
+
+  maven-pr:
+    name: Maven examples (PR)
+    runs-on: ubuntu-latest
+    # does not need publish, because there is no publishing on non-main
+    if: github.ref != 'refs/heads/main'
+    strategy:
+      fail-fast: false
+      matrix:
+        project: [jablib-examples/maven3/doi-to-bibtex]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+        with:
+          submodules: 'false'
+          show-progress: 'false'
+      - name: Set up JDK
+        uses: actions/setup-java@v5
+        with:
+          java-version: 24
+          distribution: 'corretto'
+          cache: maven
+          check-latest: true
+      - run: |
+          cd ${{ matrix.project }}
+          mvn --batch-mode --update-snapshots verify
+        shell: bash
+
   codecoverage:
     if: false
     name: Code coverage

.jbang/JabKitLauncher.java

@@ -22,19 +22,11 @@
 //SOURCES ../jabkit/src/main/java/org/jabref/toolkit/JabKit.java
 //FILES tinylog.properties=../jabkit/src/main/resources/tinylog.properties
 
-// REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
-// REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots
-//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
-// REPOS mavencentral,jitpack=https://jitpack.io
+// raw is for https://github.com/unicode-org/icu/pull/2127
+//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
 
-// TODO: ASCII things won't work, but we accept for now to keep things going
-//DEPS com.ibm.icu:icu4j:78.1
-
-// Choose one - both should work
-// https://central.sonatype.com/service/rest/repository/browse/maven-snapshots/org/jabref/jablib/
 //DEPS org.jabref:jablib:6.0-SNAPSHOT
-// https://jitpack.io/#jabref/jabref/main-SNAPSHOT
-// DEPS com.github.jabref:jabref:main-SNAPSHOT
+
 //DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3

.jbang/JabLsLauncher.java

@@ -26,16 +26,10 @@
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/LatexDefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/MarkdownDefinitionProvider.java
 
-// REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
-// REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots
-//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
-// REPOS mavencentral,jitpack=https://jitpack.io
+// raw is for https://github.com/unicode-org/icu/pull/2127
+//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
 
-// Choose one - both should work
-// https://central.sonatype.com/service/rest/repository/browse/maven-snapshots/org/jabref/jablib/
 //DEPS org.jabref:jablib:6.0-SNAPSHOT
-// https://jitpack.io/#jabref/jabref/main-SNAPSHOT
-// DEPS com.github.jabref:jabref:main-SNAPSHOT
 
 //DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
@@ -49,12 +43,14 @@
 //DEPS com.github.eclipse:lsp4j:0.24.0
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.2
+//DEPS org.eclipse.lsp4j:org.eclipse.lsp4j:0.24.0
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS org.slf4j:jul-to-slf4j:2.0.17
 //DEPS org.slf4j:slf4j-api:2.0.17
 //DEPS org.tinylog:slf4j-tinylog:2.7.0
 //DEPS org.tinylog:tinylog-impl:2.7.0
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
+//DEPS org.apache.commons:commons-lang3:3.19.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabLsLauncher {

.jbang/JabSrvLauncher.java

@@ -44,19 +44,10 @@
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/PreferencesFactory.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/Server.java
 
-// REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
-// REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots
-//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
-// REPOS mavencentral,jitpack=https://jitpack.io
+// raw is for https://github.com/unicode-org/icu/pull/2127
+//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
 
-// TODO: ASCII things won't work, but we accept for now to keep things going
-//DEPS com.ibm.icu:icu4j:78.1
-
-// Choose one - both should work
-// https://central.sonatype.com/service/rest/repository/browse/maven-snapshots/org/jabref/jablib/
 //DEPS org.jabref:jablib:6.0-SNAPSHOT
-// https://jitpack.io/#jabref/jabref/main-SNAPSHOT
-// DEPS com.github.jabref:jabref:main-SNAPSHOT
 
 //DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
@@ -92,6 +83,7 @@
 //DEPS tools.jackson.core:jackson-core:3.0.2
 //DEPS tools.jackson.core:jackson-databind:3.0.2
 //DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
+//DEPS org.apache.commons:commons-lang3:3.19.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabSrvLauncher {

CHANGELOG.md

@@ -17,13 +17,16 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- We replaced the standard ComboBox with a SearchableComboBox and added a free text field in custom Entry Types [#14082](https://github.com/JabRef/jabref/issues/14082)
+- We separated the "Clean up entries" dialog into three tabs for clarity [#13819](https://github.com/JabRef/jabref/issues/13819)
 - `JabKit`: `--porcelain` does not output any logs to the console anymore. [#14244](https://github.com/JabRef/jabref/pull/14244)
 - <kbd>Ctrl</kbd> + <kbd>Shift</kbd> + <kbd>L</kbd> now opens the terminal in the active library directory. [#14130](https://github.com/JabRef/jabref/issues/14130)
 
 ### Fixed
 
 - We fixed an issue where pressing <kbd>ESC</kbd> in the preferences dialog would not always close the dialog. [#8888](https://github.com/JabRef/jabref/issues/8888)
 - We fixed the checkbox in merge dialog "Treat duplicates the same way" to make it functional. [#14224](https://github.com/JabRef/jabref/pull/14224)
+- Correct fallback window height (786 → 768) in JabRefGUI. [#14295](https://github.com/JabRef/jabref/pull/14295)
 
 ### Removed