Merge remote-tracking branch 'upstream/main'

* upstream/main:
  Issue 13619 Make Citation relations text more clear. (#13620)
  Explain how to handle notifications (#13630)
  Fix scope of 'determine issue number' job (#13627)
  Add proper closing (#13626)
  Implement logic orchestration for Git Pull/Push operations (#13518)
  Make pattern for issue number more strict
  Fix "Cannot load file MultiMergeEntries.fxml" (#13624)
  Add Copy markdown to copy citation (#13387)
  Add ADR-0047 (#13621)
  Initial start of implementing a LSP for integrity checks (#13612)
  Refactor merge entries package structure (#13614)
  New Crowdin updates (#13616)
  BibEntry class no longer implements Cloneable (#13615)
  Fix dark mode in {} of Citation Relations tab of the entry editor (#13609)
  Update dependency org.kohsuke:github-api to v2.0-rc.4 (#13611)
  Fix setting of proxy without password (#13605)

Author: Siedlerchr

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

@@ -11,6 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     if: >
       (github.repository == 'JabRef/jabref') &&
+      (github.event.pull_request.head.repo.full_name != 'JabRef/jabref') &&
       !(
         (github.actor == 'dependabot[bot]') ||
         (

.github/workflows/tests-pr.yml

@@ -22,7 +22,7 @@ jobs:
           path: pr_number.txt
 
   check_title_format:
-    name: PR title must not start with "Fix for issue <number>"
+    name: PR title must not contain "issue <number>"
     if: github.actor != 'dependabot[bot]' && github.event.pull_request.head.repo.full_name != 'JabRef/jabref'
     runs-on: ubuntu-latest
     steps:
@@ -36,13 +36,8 @@ jobs:
           TITLE=$(gh pr view "${{ github.event.number }}" --json title --template '{{.title}}')
           echo "Title: $TITLE"
 
-          if echo "$TITLE" | grep -Eiq '^Fix for issue #?[0-9]+'; then
-            echo "❌ Title starts with 'Fix for issue <number>' — not allowed."
-            exit 1
-          fi
-
-          if echo "$TITLE" | grep -Eiq '^Fixed the issue'; then
-            echo "❌ Title starts with 'Fixed the issue' — not allowed."
+          if echo "$TITLE" | grep -Eiq 'issue ?#?[0-9]+.+'; then
+            echo "❌ Title contains 'issue <number>' — not allowed."
             exit 1
           fi
 

.jbang/CheckoutPR.java

@@ -20,7 +20,7 @@
 //JAVA 21+
 //RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
 
-//DEPS org.kohsuke:github-api:2.0-rc.3
+//DEPS org.kohsuke:github-api:2.0-rc.4
 //DEPS org.eclipse.jgit:org.eclipse.jgit.pgm:7.3.0.202506031305-r
 
 public class CheckoutPR {

.jbang/JabLsLauncher.java

@@ -0,0 +1,45 @@
+///usr/bin/env jbang "$0" "$@" ; exit $?
+
+//DESCRIPTION jabls - start a bibtex languageserver
+
+//JAVA 24
+//RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
+
+//SOURCES ../jabls-cli/src/main/java/org/jabref/languageserver/cli/ServerCli.java
+//FILES tinylog.properties=../jabls-cli/src/main/resources/tinylog.properties
+
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/LSPServer.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
+
+// 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 info.picocli:picocli:4.7.7
+//DEPS org.jspecify:jspecify:1.0.0
+
+// from jabls
+//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 org.slf4j:jul-to-slf4j:2.0.17
+//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.1
+//DEPS info.picocli:picocli:4.7.7
+//DEPS org.jabref:afterburner.fx:2.0.0
+//DEPS com.github.eclipse:lsp4j:0.24.0
+
+/// This class is required for [jbang](https://www.jbang.dev/)
+public class JabLsLauncher {
+    public static void main(String[] args) throws Exception {
+        org.jabref.languageserver.cli.ServerCli.main(args);
+    }
+}

.jbang/README.md

@@ -3,10 +3,11 @@
 This directory contains JBang scripts for JabRef.
 [JBang](https://www.jbang.dev/) allows for running Java applications without having a JDK installed (before).
 
-Three use cases:
+Four use cases:
 
 - Try out any pull request with minimal installation. See [our blog entry](https://blog.jabref.org/2025/05/31/run-pr/) for details.
 - Run JabKit - JabRef's CLI tool.
+- Run JabLs - JabRef's Language Server.
 - Run JabSrv - JabRef's HTTP server.
 
 ## Running JabKit without installation
@@ -16,8 +17,8 @@ By using [gg.cmd](https://github.com/eirikb/gg#ggcmd) you can "just run" JabKit
 1. Download `gg.cmd` from: <https://github.com/eirikb/gg#ggcmd>. `gg.cmd` is a "binary" running on macOS, Linux, and Windows. No need for different binaries on different operating systems.
 2. Run `gg.cmd`. This will download and use JBang as wrapper around running JabKit:
 
-    - Linux/macOS: Run `sh ./gg.cmd jbang jabkit@jabref --help`.
-    - Windows: Run `gg.cmd jbang jabkit@jabref --help`.
+    - Linux/macOS: Run `sh ./gg.cmd jbang jabkit@jabref`.
+    - Windows: Run `gg.cmd jbang jabkit@jabref`.
 
 You can also put `gg.cmd` on your `PATH` and make it executable.
 Then you enable `alias jabkit='gg.cmd jbang jabkit@jabref`.
@@ -27,27 +28,57 @@ Then you enable `alias jabkit='gg.cmd jbang jabkit@jabref`.
 If you have JBang installed, just run
 
 ```terminal
-jbang jabkit@jabref --help
+jbang jabkit@jabref
 ```
 
 You can also install `jabkit` permanently in your `PATH`:
 
 1. [Install JBang](https://www.jbang.dev/download/). E.g., by `brew install jbangdev/tap/jbang` or `choco install jbang`
 2. Make `jabkit` available on the command line: `jbang app install jabkit@jabref`
-3. Run `jabkit --help`
+3. Run `jabkit`
 
 [JBang takes care about updating JabKit automatically](https://github.com/orgs/jbangdev/discussions/1636#discussioncomment-6150992).
 
+## Running JabLs
+
+If you have JBang installed, just run following command
+
+```terminal
+jbang jabls@jabref
+```
+
+With `gg.cmd`:
+
+```terminal
+sh ./gg.cmd jbang jabls@jabref
+```
+
+With `npx`:
+
+```terminal
+npx @jbangdev/jbang jabls@jabref
+```
+
+One can add `--help` to see available options.
+
 ## Running JabSrv
 
 If you have JBang installed, just run following command
 
 ```terminal
-jbang jabsrv@jabref --help
+jbang jabsrv@jabref
 ```
 
 With `gg.cmd`:
 
 ```terminal
-sh ./gg.cmd jbang jabsrv@jabref --help
+sh ./gg.cmd jbang jabsrv@jabref
 ```
+
+With `npx`:
+
+```terminal
+npx @jbangdev/jbang jabsrv@jabref
+```
+
+One can add `--help` to see available options. E.g., how to set another port and how to specify served libraries.

CHANGELOG.md

@@ -21,10 +21,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added the field `monthfiled` to the default list of fields to resolve BibTeX-Strings for [#13375](https://github.com/JabRef/jabref/issues/13375)
 - We added a new ID based fetcher for [EuropePMC](https://europepmc.org/). [#13389](https://github.com/JabRef/jabref/pull/13389)
 - We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)
+- We added "copy preview as markdown" feature. [#12552](https://github.com/JabRef/jabref/issues/12552)
 - In case no citation relation information can be fetched, we show the data providers reason. [#13549](https://github.com/JabRef/jabref/pull/13549)
 
 ### Changed
 
+- We changed Citation Relations tab and gave tab panes more descriptive titles and tooltips. [#13619](https://github.com/JabRef/jabref/issues/13619)
 - We changed the name from Open AI Provider to Open AI (or API compatible). [#13585](https://github.com/JabRef/jabref/issues/13585)
 - We improved the citations relations caching by implementing an offline storage. [#11189](https://github.com/JabRef/jabref/issues/11189)
 - We added a tooltip to keywords that resemble Math Subject Classification (MSC) codes. [#12944](https://github.com/JabRef/jabref/issues/12944)
@@ -65,6 +67,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- We fixed dark mode of BibTeX Source dialog in Citation Relations tab. [#13599](https://github.com/JabRef/jabref/issues/13599)
 - We fixed an issue where the LibreOffice integration did not support citation keys containing Unicode characters. [#13301](https://github.com/JabRef/jabref/issues/13301)
 - We fixed an issue where the "Search ShortScience" action did not convert LaTeX-formatted titles to Unicode.[#13418](https://github.com/JabRef/jabref/issues/13418)
 - We added a fallback for the "Convert to biblatex" cleanup when it failed to populate the `date` field if `year` contained a full date in ISO format (e.g., `2011-11-11`). [#11868](https://github.com/JabRef/jabref/issues/11868)
@@ -78,6 +81,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the preview area in the "Select Style" dialog of the LibreOffice integration was too small to display full content. [#13051](https://github.com/JabRef/jabref/issues/13051)
 - We excluded specific fields (e.g., `comment`, `pdf`, `sortkey`) from the consistency check to reduce false positives [#13131](https://github.com/JabRef/jabref/issues/13131)
 - We fixed an issue where moved or renamed linked files in the file directory were not automatically relinked by the “search for unlinked files” feature. [#13264](https://github.com/JabRef/jabref/issues/13264)
+- We fixed an issue with proxy setup in the absence of a password. [#12412](https://github.com/JabRef/jabref/issues/12412)
 - We fixed an issue where the tab showing the fulltext search results was not displayed. [#12865](https://github.com/JabRef/jabref/issues/12865)
 - We fixed an issue showing an empty tooltip in maintable. [#11681](https://github.com/JabRef/jabref/issues/11681)
 - We fixed an issue displaying a warning if a file to open is not found. [#13430](https://github.com/JabRef/jabref/pull/13430)

build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts

@@ -285,6 +285,70 @@ extraJavaModuleInfo {
     module("com.github.javaparser:javaparser-symbol-solver-core", "com.github.javaparser.symbolsolver.core")
     module("net.sf.jopt-simple:jopt-simple", "jopt.simple")
 
+    // "com.github.eclipse:org.eclipse.lsp4j", "lsp4j"
+    //   - The name 'org.eclipse.lsp4j' is different than the name derived from the Jar file name 'lsp4j'; turn off 'failOnModifiedDerivedModuleNames' or explicitly allow override via 'overrideModuleName()'
+    //   - Not a module and no mapping defined: lsp4j-0.24.0.jar
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j", "lsp4j") {
+        overrideModuleName()
+        exportAllPackages()
+        requireAllDefinedDependencies()
+        // Note the missing "lsp4j" at the group
+        mergeJar("com.github.eclipse:lsp4j")
+        requires("com.google.gson")
+
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.debug", "lsp4j.debug") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.generator", "lsp4j.generator") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.jsonrpc", "lsp4j.jsonrpc") {
+        overrideModuleName()
+        exportAllPackages()
+        requires("com.google.gson")
+        requires("java.logging")
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.jsonrpc.debug", "lsp4j.jsonrpc.debug") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.websocket", "lsp4j.websocket") {
+        overrideModuleName()
+        exportAllPackages()
+        requireAllDefinedDependencies()
+    }
+    module("com.github.eclipse.lsp4j:org.eclipse.lsp4j.websocket.jakarta", "lsp4j.websocket.jakarta") {
+        overrideModuleName()
+        exportAllPackages()
+        requireAllDefinedDependencies()
+    }
+    module("jakarta.websocket:jakarta.websocket-api", "jakarta.websocket") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("javax.websocket:javax.websocket-api", "javax.websocket") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("org.eclipse.xtend:org.eclipse.xtend", "xtend") {
+        exportAllPackages()
+    }
+    module("org.eclipse.xtend:org.eclipse.xtend.lib", "xtend.lib") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("org.eclipse.xtend:org.eclipse.xtend.lib.macro", "xtend.lib.macro") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+    module("org.eclipse.xtext:org.eclipse.xtext.xbase.lib", "xtext.xbase.lib") {
+        overrideModuleName()
+        exportAllPackages()
+    }
+
     module("com.tngtech.archunit:archunit-junit5-api", "com.tngtech.archunit.junit5.api") {
         exportAllPackages()
         requireAllDefinedDependencies()

build-logic/src/main/kotlin/org.jabref.gradle.feature.test.gradle.kts

@@ -28,8 +28,8 @@ testlogger {
     showPassed = false
     showSkipped = false
 
-    showCauses = false
-    showStackTraces = false
+    showCauses = true
+    showStackTraces = true
 }
 
 configurations.testCompileOnly {

build.gradle.kts

@@ -37,6 +37,7 @@ rewrite {
 requirementTracing {
     inputDirectories.setFrom(files("docs",
             "jablib/src/main/java", "jablib/src/test/java",
+            "jabls/src/main/java", "jabls/src/test/java",
             "jabkit/src/main/java", "jabkit/src/test/java",
             "jabgui/src/main/java", "jabgui/src/test/java",
             "jabsrv/src/main/java", "jabsrv/src/test/java"

docs/code-howtos/git.md

@@ -0,0 +1,105 @@
+# Git
+
+## Why Semantic Merge?
+
+In JabRef, we aim to minimize user interruptions when collaborating on the same `.bib` library file using Git. To achieve this, we go beyond Git’s default line-based syntactic merging and implement our own semantic merge logic that understands the structure of BibTeX entries.
+
+This means:
+
+* Even if Git detects conflicting lines,
+* JabRef is able to recognize that both sides are editing the same BibTeX entry,
+* And determine—at the field level—whether there is an actual semantic conflict.
+
+## Merge Example
+
+The following example illustrates a case where Git detects a conflict, but JabRef is able to resolve it automatically.
+
+### Base Version
+
+```bibtex
+@article{a,
+  author = {don't know the author},
+  doi = {xya},
+}
+
+@article{b,
+  author = {don't know the author},
+  doi = {xyz},
+}
+```
+
+### Bob's Side
+
+Bob reorders the entries and updates the author field of entry b:
+
+```bibtex
+@article{b,
+  author = {author-b},
+  doi = {xyz},
+}
+
+@article{a,
+  author = {don't know the author},
+  doi = {xya},
+}
+```
+
+### Alice's Side
+
+Alice modifies the author field of entry a:
+
+```bibtex
+@article{a,
+  author = {author-a},
+  doi = {xya},
+}
+
+@article{b,
+  author = {don't know the author},
+  doi = {xyz},
+}
+```
+
+### Merge Outcome
+
+When Alice runs git pull, Git sees that both branches have modified overlapping lines (due to reordering and content changes) and reports a syntactic conflict.
+
+However, JabRef is able to analyze the entries and determine that:
+
+* Entry a was modified only by Alice.
+* Entry b was modified only by Bob.
+* There is no conflict at the field level.
+* The order of entries in the file does not affect BibTeX semantics.
+
+Therefore, JabRef performs an automatic merge without requiring manual conflict resolution.
+
+## Related Test Cases
+
+The semantic conflict detection and merge resolution logic is covered by:
+
+* `org.jabref.logic.git.util.SemanticMergerTest#patchDatabase`
+* `org.jabref.logic.git.util.SemanticConflictDetectorTest#semanticConflicts`.
+
+## Conflict Scenarios
+
+The following table describes when semantic merge in JabRef should consider a situation as conflict or not during a three-way merge.
+
+| ID   | Base                       | Local Change                       | Remote Change                      | Result |
+|------|----------------------------|------------------------------------|------------------------------------|--------|
+| T1   | Field present              | (unchanged)                        | Field modified                     | No conflict. The local version remained unchanged, so the remote change can be safely applied. |
+| T2   | Field present              | Field modified                     | (unchanged)                        | No conflict. The remote version did not touch the field, so the local change is preserved. |
+| T3   | Field present              | Field changed to same value        | Field changed to same value        | No conflict. Although both sides changed the field, the result is identical—therefore, no conflict. |
+| T4   | Field present              | Field changed to A                 | Field changed to B                 | Conflict. This is a true semantic conflict that requires resolution. |
+| T5   | Field present              | Field deleted                      | Field modified                     | Conflict. One side deleted the field while the other updated it—this is contradictory. |
+| T6   | Field present              | Field modified                     | Field deleted                      | Conflict. Similar to T5, one side deletes, the other edits—this is a conflict. |
+| T7   | Field present              | (unchanged)                        | Field deleted                      | No conflict. Local did not modify anything, so remote deletion is accepted. |
+| T8   | Entry with fields A and B  | Field A modified                   | Field B modified                   | No conflict. Changes are on separate fields, so they can be merged safely. |
+| T9   | Entry with fields A and B  | Field order changed                | Field order changed differently    | No conflict. Field order is not semantically meaningful, so no conflict is detected. |
+| T10  | Entries A and B            | Entry A modified                   | Entry B modified                   | No conflict. Modifications are on different entries, which are always safe to merge. |
+| T11  | Entry with existing fields | (unchanged)                        | New field added                    | No conflict. Remote addition can be applied without issues. |
+| T12  | Entry with existing fields | New field added with value A       | New field added with value B       | Conflict. One side added while the other side modified—there is a semantic conflict. |
+| T13  | Entry with existing fields | New field added                    | (unchanged)                        | No conflict. Safe to preserve the local addition. |
+| T14  | Entry with existing fields | New field added with value A       | New field added with value A       | No conflict. Even though both sides added it, the value is the same—no need for resolution. |
+| T15  | Entry with existing fields | New field added with value A       | New field added with value B       | Conflict. The same field is introduced with different values, which creates a conflict. |
+| T16  | (entry not present)        | New entry with author A            | New entry with author B            | Conflict. Both sides created a new entry with the same citation key, but the fields differ. |
+| T17  | (entry not present)        | New entry with identical fields    | New entry with identical fields    | No conflict. Both sides created a new entry with the same citation key and identical fields, so it can be merged safely. |