Merge branch 'main' into feat-ai-chat-copy-menu

Author: pulkitbajaj

.github/ghprcomment.yml

@@ -46,9 +46,6 @@
     IntelliJ auto format covers some cases.
     There seem to be issues with your code style and autoformat configuration.
     Please reformat your code (<kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>L</kbd>) and commit, then push.
-
-
-    In special cases, consider using `// formatter:off` and `// formatter:on` annotations to allow deviation from the code style.
 - jobName: Checkstyle
   workflowName: 'Source Code Tests'
   message: >

.github/workflows/check-links.yml

@@ -15,6 +15,10 @@ concurrency:
   group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
+permissions:
+  contents: read
+  pull-requests: write
+
 jobs:
   check-links:
     if: github.repository == 'JabRef/jabref'

.github/workflows/stale.yml

@@ -35,18 +35,32 @@ jobs:
           days-before-pr-close: 7
           close-pr-message: >
             This PR is being closed due to continued inactivity.
-      - name: Output result
-        run: echo "${{ steps.stale.outputs.closed-issues-prs }}" >> $GITHUB_STEP_SUMMARY
       - name: Process closed issues/PRs
         if: ${{ steps.stale.outputs.closed-issues-prs != '[]' }}
         env:
-          CLOSED: ${{ steps.stale.outputs.closed-issues-prs }}
+          CLOSED_JSON: ${{ steps.stale.outputs.closed-issues-prs }}
         run: |
-          echo ${{ steps.stale.outputs.closed-issues-prs }}
-          # CLOSED is comma-separated like: "12,34,56"
-          IFS=',' read -r -a nums <<< "${CLOSED}"
-          for n in "${nums[@]}"; do
+          echo "Raw payload:"
+          cat <<EOF
+          ${{ steps.stale.outputs.closed-issues-prs }}
+          EOF
+
+          echo "PR numbers:"
+          echo "$CLOSED_JSON" | jq -r '.[] | select(.pull_request != null) | .number' | while read -r n; do
             [ -n "$n" ] || continue
             echo "Handling #$n"
-            gh workflow run "On PR closed" --ref main --field pr_number=$n
+            gh workflow run "On PR closed" --ref main --field pr_number="$n"
           done
+      - name: Write closed PR URLs to summary
+        if: always()
+        env:
+          CLOSED_JSON: ${{ steps.stale.outputs.closed-issues-prs }}
+        run: |
+          {
+            echo "## Closed PRs"
+            echo
+            echo "$CLOSED_JSON" \
+              | jq -r '.[] | select(.pull_request != null) | "- [#\(.number)](\(.pull_request.html_url))"' \
+              || true
+            echo
+          } >> "$GITHUB_STEP_SUMMARY"

.jbang/JabLsLauncher.java

@@ -16,6 +16,7 @@
 // from jabls
 //DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
 //DEPS info.picocli:picocli:4.7.7
+//DEPS org.apache.commons:commons-lang3:3.20.0
 //DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.3
 //DEPS org.eclipse.lsp4j:org.eclipse.lsp4j:0.24.0
 //DEPS org.slf4j:jul-to-slf4j:2.0.17

.jbang/JabSrvLauncher.java

@@ -22,7 +22,7 @@
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.postgresql:postgresql:42.7.8
 //DEPS org.bouncycastle:bcprov-jdk18on:1.83
-//DEPS com.konghq:unirest-modules-gson:4.7.0
+//DEPS com.konghq:unirest-modules-gson:4.7.1
 //DEPS jakarta.ws.rs:jakarta.ws.rs-api:4.0.0
 //DEPS org.glassfish.jersey.core:jersey-server:4.0.0
 //DEPS org.glassfish.jersey.inject:jersey-hk2:4.0.0
@@ -34,11 +34,11 @@
 //DEPS org.glassfish.grizzly:grizzly-framework:4.0.2
 //DEPS jakarta.validation:jakarta.validation-api:3.1.1
 //DEPS org.hibernate.validator:hibernate-validator:9.1.0.Final
-//DEPS com.konghq:unirest-modules-gson:4.7.0
+//DEPS com.konghq:unirest-modules-gson:4.7.1
 //DEPS com.google.guava:guava:33.5.0-jre
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.5.0
-//DEPS de.undercouch:citeproc-java:3.4.0
+//DEPS de.undercouch:citeproc-java:3.4.1
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 //DEPS tools.jackson.core:jackson-core:3.0.3
 //DEPS tools.jackson.core:jackson-databind:3.0.3

AGENTS.md

@@ -1,7 +1,7 @@
 ## Our policy
 
 > [!IMPORTANT]
-> This project does not accept fully AI-generated pull requests. AI tools may be used assistively only. You must understand and take responsibility for every change you submit.
+> This project does not accept fully AI-generated pull requests. AI tools may only be used for assistance. You must understand and take responsibility for every change you submit.
 
 This `AGENTS.md` file acts as a set of instructions that some AI coding tools can read. For more information please read our [AI policy](./CONTRIBUTING.md#ai-usage-policy).
 
@@ -60,7 +60,7 @@ Agents **must not**:
    BAD: new HashSet<>(Arrays.asList(...))
    GOOD: Set.of(...)
 - Java 21 introduced SequencedCollection and SequencedSet interfaces. Use it instead of LinkedHashSet (where applicable)
-- To create an empty list we use `List.of()` instead of `Collections.emptyList()`.
+- To create an empty list or map we use `List.of()` and `Map.of()` instead of `Collections.emptyList()` and `Collections.emptyMap()`.
 - Correctly spelled variable names (meaning: no typos in variable names).
 - Use StringJoiner instead of StringBuilder (if possible)
 - Prefer immutability and explicit nullability (JSpecify)

CHANGELOG.md

@@ -11,16 +11,23 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We fixed an issue where a redundant validation listener was causing duplicate error dialogs when invalid BibTeX source was detected in the SourceTab. [#14805](https://github.com/JabRef/jabref/issues/14805)
 - We added support for selecting citation fetcher in Citations Tab. [#14430](https://github.com/JabRef/jabref/issues/14430)
 - In the "New Entry" dialog the identifier type is now automatically updated on typing. [#14660](https://github.com/JabRef/jabref/issues/14660)
 - We added the ability to copy selected text from AI chat interface. [#14655](https://github.com/JabRef/jabref/issues/14655)
+- We added cover images for books, which will display in entry previews if available, and can be automatically downloaded when adding an entry via ISBN. [#10120](https://github.com/JabRef/jabref/issues/10120)
 
 ### Changed
 
 ### Fixed
 
+- Fixed localized walkthrough highlight for 'Preferences' menu item. [#14822](https://github.com/JabRef/jabref/issues/14822)
+- We Improved detection of arXiv identifiers when pasting arXiv URLs that include URL fragments. [#14659](https://github.com/JabRef/jabref/issues/14659)
 - We fixed an error on startup when using portable preferences. [#14729](https://github.com/JabRef/jabref/issues/14729)
 - We fixed an issue when warning for duplicate entries in the "New Entry" dialog. [#14662](https://github.com/JabRef/jabref/pull/14662)
+- We fixed the Quality > Automatically set file links button. Now if a file is moved, the button can relink the moved file to the broken linked file. [#9798](https://github.com/JabRef/jabref/issues/9798)
+- We fixed an issue where JabRef would not start on Linux ARM due to missing binaries for postgres-embedded [#14783](https://github.com/JabRef/jabref/issues/14783)
+- We fixed an issue where JaRef would not correctly remember the opened side panels in the preferences [#14818](https://github.com/JabRef/jabref/issues/14818)
 
 ### Removed
 
@@ -36,7 +43,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added 15 non-standard BibLaTeX entry types (Audio, Image, Legal, ...) to the group "Non-standard types" group in the New Entry dialog and in the context menu. [#12963](https://github.com/JabRef/jabref/issues/12963)
 - We added a drop-down menu to those custom fields in the main table for which content selector values exists. [#14087](https://github.com/JabRef/jabref/issues/14087)
 - We added a "Jump to Field" dialog (`Ctrl+J`) to quickly search for and navigate to any field across all tabs. [#12276](https://github.com/JabRef/jabref/issues/12276).
-- We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
+- We added "IEEE" as another option for parsing plain text citations. [#14233](https://github.com/JabRef/jabref/pull/14233)
 - We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
 - We added `doi-to-bibtex` to `JabKit`. [#14244](https://github.com/JabRef/jabref/pull/14244)
 - We added `--provider=crossref` to `get-cited-works` at `JabKit`. [#14357](https://github.com/JabRef/jabref/pull/14357)

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright © 2003-2025 JabRef Authors
+Copyright © 2003-2026 JabRef Authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal