Merge branch 'fix-group-icons' of github.com:geovani-rocha/jabref into fix-group-icons

* 'fix-group-icons' of github.com:geovani-rocha/jabref: (26 commits)
  chore(deps): update dependency org.apache.logging.log4j:log4j-to-slf4j to v2.25.4 (JabRef#15436)
  chore(deps): update jackson monorepo to v3.1.1 (JabRef#15435)
  Fix PushToPreferences reset and import (JabRef#15395)
  Add fulltext fetcher for Wiley via their TDM API (JabRef#15388)
  Embed in-text nature in reference marks for CSL citations (JabRef#15381)
  Chore(deps): Bump com.gradleup.shadow:shadow-gradle-plugin (JabRef#15430)
  Fix not on fx thread exceptions for cleanup and cite key generator (JabRef#15424)
  Revert "Update gradle to nightly of 2026-03-23 (JabRef#15372)"
  feat: add benchmarks for Lucene fulltext search and linked file indexing, including setup and teardown of the index. (JabRef#15385)
  Chore(deps): Bump org.openrewrite.recipe:rewrite-recipe-bom (JabRef#15418)
  Add claude gitignore (JabRef#15413)
  Fix group filter icon in side pane (JabRef#15408)
  Add new prs_link feature
  Chore(deps): Bump org.glassfish.hk2:hk2-api in /versions (JabRef#15422)
  Chore(deps): Bump org.openrewrite.rewrite from 7.28.2 to 7.29.0 (JabRef#15419)
  Chore(deps): Bump jablib/src/main/resources/csl-styles (JabRef#15417)
  Fix for inconsistent "hide tab bar" behavior (JabRef#15409)
  Update dependency org.glassfish.hk2:hk2-utils to v4 (JabRef#15407)
  Persist file notifications (JabRef#15403)
  Update dependency org.glassfish.hk2:hk2-locator to v4 (JabRef#15405)
  ...

Author: Siedlerchr

.github/workflows/dockerimages.yml

@@ -22,7 +22,6 @@ permissions:
 
 jobs:
   build:
-    if: github.repository == 'JabRef/jabref'
     strategy:
       max-parallel: 1
       matrix:
@@ -34,14 +33,14 @@ jobs:
         uses: docker/metadata-action@v6
         with:
           images: |
-            ghcr.io/JabRef/${{ matrix.component }}
+            ghcr.io/${{ github.repository_owner }}/${{ matrix.component }}
           tags: |
             type=schedule,pattern={{date 'YYYY-MM-DD'}}
             type=ref,event=tag
             type=edge,branch=main
             type=ref,event=pr
           labels: |
-            org.opencontainers.image.source=https://github.com/JabRef/jabref
+            org.opencontainers.image.source=https://github.com/${{ github.repository }}
             org.opencontainers.image.title=${{ matrix.component }}
             org.opencontainers.image.description=${{ matrix.component == 'jabkit' && 'JabRef''s CLI tool' || 'JabRef''s HTTP server' }}
       - name: Login to GitHub Container Registry

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

@@ -71,7 +71,7 @@ jobs:
             If not, our [contributing guidelines](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) is the place you should go to.
 
 
-            At this point in time, you raised {{ prs_total }} pull request(s) of which {{ prs_merged_percentage }}% ({{ prs_merged }}/{{ prs_total }}) have been merged.
+            At this point in time, you raised {{ prs_total }} pull request(s) of which {{ prs_merged_percentage }}% ({{ prs_merged }}/[{{ prs_total }}]({{ prs_link }})) have been merged.
           # If this is updated, also update the number at unassign-issues.yml
           days_until_unassign: 14
           self_unassigned_text: |

.gitignore

@@ -1,3 +1,7 @@
+# AI tooling
+
+.claude/
+
 # no generated files in version control
 src/main/gen/
 src/main/generated/

.jbang/JabLsLauncher.java

@@ -17,7 +17,7 @@
 //DEPS com.fasterxml.jackson.core:jackson-annotations:2.21
 //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.apache.logging.log4j:log4j-to-slf4j:2.25.4
 //DEPS org.eclipse.lsp4j:org.eclipse.lsp4j:1.0.0
 //DEPS org.slf4j:jul-to-slf4j:2.0.17
 //DEPS org.slf4j:slf4j-api:2.0.17

.jbang/JabSrvLauncher.java

@@ -25,7 +25,7 @@
 //DEPS jakarta.validation:jakarta.validation-api:3.1.1
 //DEPS net.harawata:appdirs:1.5.0
 //DEPS org.apache.commons:commons-lang3:3.20.0
-//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.3
+//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.4
 //DEPS org.bouncycastle:bcprov-jdk18on:1.83
 //DEPS org.postgresql:postgresql:42.7.10
 //DEPS org.slf4j:slf4j-api:2.0.17
@@ -34,17 +34,17 @@
 //DEPS org.tinylog:tinylog-impl:2.7.0
 //DEPS org.glassfish.grizzly:grizzly-framework:5.0.0
 //DEPS org.glassfish.grizzly:grizzly-http-server:5.0.0
-//DEPS org.glassfish.hk2:hk2-api:3.1.1
-//DEPS org.glassfish.hk2:hk2-locator:3.1.1
-//DEPS org.glassfish.hk2:hk2-utils:3.1.1
+//DEPS org.glassfish.hk2:hk2-api:4.0.0
+//DEPS org.glassfish.hk2:hk2-locator:4.0.0
+//DEPS org.glassfish.hk2:hk2-utils:4.0.0
 //DEPS org.glassfish.jersey.containers:jersey-container-grizzly2-http:4.0.2
 //DEPS org.glassfish.jersey.core:jersey-server:4.0.2
 //DEPS org.glassfish.jersey.inject:jersey-hk2:4.0.2
 //DEPS org.hibernate.validator:hibernate-validator:9.1.0.Final
 //DEPS org.jabref:afterburner.fx:2.0.0
-//DEPS tools.jackson.core:jackson-core:3.1.0
-//DEPS tools.jackson.core:jackson-databind:3.1.0
-//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.1.0
+//DEPS tools.jackson.core:jackson-core:3.1.1
+//DEPS tools.jackson.core:jackson-databind:3.1.1
+//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.1.1
 
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/BibEntryDTO.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/cayw/SimpleJson.java

.linkspector.yml

@@ -16,3 +16,5 @@ ignorePatterns:
   - pattern: "dl\\.acm\\.org"
   # works locally, but not in the checker
   - pattern: "^https://www.pdflib.com/pdf-knowledge-base/xmp/free-xmp-validator"
+  # Automated access blocked by Cloudflare, see issue for context: https://github.com/JabRef/jabref/issues/13404
+  - pattern: "onlinelibrary\\.wiley\\.com"

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added support for downloading full-text PDFs from Wiley journals via the Wiley TDM API. [#13404](https://github.com/JabRef/jabref/issues/13404)
 - We added `--key-patterns` option to CLI parameters to allows users to set a citation key's pattern for a specific entry type. [#14707](https://github.com/JabRef/jabref/issues/14707)
 - We added a CLI option `--field-formatters` to the `convert` and `generate-bib-from-aux` commands to apply field formatters during export. [#11520](https://github.com/JabRef/jabref/issues/11520)
 - We added a preference to skip the import dialog for entries received from browser extensions, allowing direct import into the current library. The import dialog is shown by default; users can enable direct import in Preferences.
@@ -24,6 +25,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- We changed the groups filter field to use a filter icon. [#15402](https://github.com/JabRef/jabref/issues/15402)
 - We improved the MultiMergeEntries dialog to automatically select the most plausible field value when merging entries (e.g. a more specific date). [#15027](https://github.com/JabRef/jabref/issues/15027)
 - We removed the restart prompt when accepting Mr. DLib privacy settings or hiding the Related articles tab in the entry editor. [#15195](https://github.com/JabRef/jabref/issues/15195)
 - We replaced the unlinked files dialog with a wizard-based interface for searching and importing files. [#12709](https://github.com/JabRef/jabref/issues/12709)
@@ -39,6 +41,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- We fixed an issue where the side pane (Groups/Web search) width was not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
+- We fixed the ScienceDirect fulltext fetcher not returning a PDF when the Elsevier API response includes a direct PDF link. [#12161](https://github.com/JabRef/jabref/issues/12161)
 - We fixed vertical cursor movement shortcuts (Command+Up/Down for document start/end, Option+Up/Down for paragraph start/end) not working correctly in the BibTeX source editor on macOS. [#5937](https://github.com/JabRef/jabref/issues/5937)
 - We fixed text cursor movement shortcuts (Command+Left/Right for line start/end, Option+Left/Right for word navigation) not working correctly in the BibTeX source editor on macOS. [#5937](https://github.com/JabRef/jabref/issues/5937)
 - We fixed PDF import to prefer the content extracted title over filename like XMP metadata titles. [#11999](https://github.com/JabRef/jabref/issues/11999)
@@ -65,8 +69,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where an exception would be thrown when trying to extract references from a PDF [#15308](https://github.com/JabRef/jabref/pull/15308)
 - We fixed an issue where an exception was thrown when importing via cli and no opened library. [#15314](https://github.com/JabRef/jabref/pull/15314)
 - We fixed an issue where the Citation Relations tab failed to recognize already-imported papers when their DOI differed only in letter casing. [#12967](https://github.com/JabRef/jabref/issues/12967)
+- We fixed an issue where a tab or the tab bar would not show, while the setting "hide tab bar when a single library is present" was toggled off [#12680](https://github.com/JabRef/jabref/issues/12680)
 - We improved CSL support with JabRef LibreOffice converter extension. [#14387](https://github.com/JabRef/jabref/issues/14387)
 - We fixed an issue where a search group would not be updated in the ui after an entry change [#13378](https://github.com/JabRef/jabref/issues/13378)
+- We fixed an issue where a search group would not be updated in the ui after an entry change [#15386](https://github.com/JabRef/jabref/issues/15386)
+- We fixed exceptions occuring when generating citation keys or using certain cleanup operations on macOS [#15366](https://github.com/JabRef/jabref/issues/15366)
 
 ### Removed
 

Dockerfile.jabkit

@@ -1,7 +1,7 @@
-FROM maven:3.9.12-amazoncorretto-25-debian AS build
+FROM maven:3.9.14-amazoncorretto-25-debian AS build
 
 # Is not debian-based
-# FROM amazoncorretto:25-jdk AS build
+# FROM amazoncorretto:26-jdk AS build
 
 ARG VERSION="100.0.0"
 ARG VERSION_INFO="100.0.0"
@@ -32,16 +32,27 @@ COPY jabls-cli/build.gradle.kts jabls-cli/
 COPY jabsrv/build.gradle.kts jabsrv/
 COPY jabsrv-cli/build.gradle.kts jabsrv-cli/
 COPY test-support test-support
+COPY ./jabgui/src/main/java/module-info.java ./jabgui/src/main/java/module-info.java
+COPY ./jabkit/src/main/java/module-info.java ./jabkit/src/main/java/module-info.java
+COPY ./jablib/src/main/java/module-info.java ./jablib/src/main/java/module-info.java
+COPY ./jabls/src/main/java/module-info.java ./jabls/src/main/java/module-info.java
+COPY ./jabls-cli/src/main/java/module-info.java ./jabls-cli/src/main/java/module-info.java
+COPY ./jabsrv/src/main/java/module-info.java ./jabsrv/src/main/java/module-info.java
+COPY ./jabsrv-cli/src/main/java/module-info.java ./jabsrv-cli/src/main/java/module-info.java
+COPY ./test-support/src/main/java/module-info.java ./test-support/src/main/java/module-info.java
+
 COPY versions versions
 
 # Cache gradle and build-logic
 RUN ./gradlew --no-daemon :build-logic:jar
 
 COPY . .
 
-RUN ./gradlew --no-daemon -PprojVersion="${VERSION}" -PprojVersionInfo="${VERSION_INFO}" -Ptagbuild="${TAG_BUILD}" :jabkit:jpackage && \
-    mkdir /dist && \
-    mv jabkit/build/packages/*/* /dist
+RUN ./gradlew --no-daemon -PprojVersion="${VERSION}" -PprojVersionInfo="${VERSION_INFO}" -Ptagbuild="${TAG_BUILD}" :jabkit:jpackage
+
+RUN mkdir /dist
+
+RUN mv jabkit/build/packages/*/* /dist
 
 
 # jpackage needs glibc; alpine does not work

Dockerfile.jabsrv

@@ -1,7 +1,7 @@
-FROM maven:3.9.12-amazoncorretto-25-debian AS build
+FROM maven:3.9.14-amazoncorretto-25-debian AS build
 
 # Is not debian-based
-# FROM amazoncorretto:25-jdk AS build
+# FROM amazoncorretto:26-jdk AS build
 
 ARG VERSION="100.0.0"
 ARG VERSION_INFO="100.0.0"
@@ -32,16 +32,27 @@ COPY jabls-cli/build.gradle.kts jabls-cli/
 COPY jabsrv/build.gradle.kts jabsrv/
 COPY jabsrv-cli/build.gradle.kts jabsrv-cli/
 COPY test-support test-support
+COPY ./jabgui/src/main/java/module-info.java ./jabgui/src/main/java/module-info.java
+COPY ./jabkit/src/main/java/module-info.java ./jabkit/src/main/java/module-info.java
+COPY ./jablib/src/main/java/module-info.java ./jablib/src/main/java/module-info.java
+COPY ./jabls/src/main/java/module-info.java ./jabls/src/main/java/module-info.java
+COPY ./jabls-cli/src/main/java/module-info.java ./jabls-cli/src/main/java/module-info.java
+COPY ./jabsrv/src/main/java/module-info.java ./jabsrv/src/main/java/module-info.java
+COPY ./jabsrv-cli/src/main/java/module-info.java ./jabsrv-cli/src/main/java/module-info.java
+COPY ./test-support/src/main/java/module-info.java ./test-support/src/main/java/module-info.java
+
 COPY versions versions
 
 # Cache gradle and build-logic
 RUN ./gradlew --no-daemon :build-logic:jar
 
 COPY . .
 
-RUN ./gradlew --no-daemon -PprojVersion="${VERSION}" -PprojVersionInfo="${VERSION_INFO}" -Ptagbuild="${TAG_BUILD}" :jabsrv-cli:jpackage && \
-    mkdir /dist && \
-    mv jabsrv-cli/build/packages/*/* /dist
+RUN ./gradlew --no-daemon -PprojVersion="${VERSION}" -PprojVersionInfo="${VERSION_INFO}" -Ptagbuild="${TAG_BUILD}" :jabsrv-cli:jpackage
+
+RUN mkdir /dist
+
+RUN mv jabsrv-cli/build/packages/*/* /dist
 
 
 # jpackage needs glibc; alpine does not work

build-logic/build.gradle.kts

@@ -10,8 +10,8 @@ repositories {
 dependencies {
     implementation("com.adarshr:gradle-test-logger-plugin:4.0.0")
     implementation("com.autonomousapps:dependency-analysis-gradle-plugin:3.6.1")
-    implementation("com.github.andygoossens:gradle-modernizer-plugin:1.12.0")
-    implementation("com.gradleup.shadow:shadow-gradle-plugin:9.4.0")
+    implementation("com.github.andygoossens:gradle-modernizer-plugin:1.13.0")
+    implementation("com.gradleup.shadow:shadow-gradle-plugin:9.4.1")
     implementation("de.undercouch.download:de.undercouch.download.gradle.plugin:5.7.0")
     implementation("org.gradlex:extra-java-module-info:1.14")
     implementation("org.gradlex:java-module-dependencies:1.12.1")