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

* upstream/main: (25 commits)
  Remove remainging "testLogging" (#10769)
  Reuse JUnit 5.7's @DisabledIfEnvironmentVariable (#10768)
  Refactored LibraryTab (#10732)
  Fix annotation (#10766)
  Add initial .git-blame-ignore-revs (#10765)
  Streamline test output (#10762)
  Fix NPE when opening and re-opening a library (#10763)
  Changed default status of 'Automatically open folder of attached files' (#10748)
  Implement test cases for search (#10193)
  Add cites field to bib entries for citation relation (#10752)
  Ignore submodule changes (for normal devs) (#10754)
  Fix line endings
  Bump lycheeverse/lychee-action from 1.8.0 to 1.9.0 (#10760)
  Bump appleboy/ssh-action from 1.0.2 to 1.0.3 (#10761)
  Bump org.apache.lucene:lucene-core from 9.9.0 to 9.9.1 (#10759)
  Bump org.openrewrite.rewrite from 6.5.4 to 6.6.3 (#10758)
  Bump org.glassfish.jersey.containers:jersey-container-grizzly2-http (#10755)
  Bump org.jsoup:jsoup from 1.16.2 to 1.17.2 (#10756)
  Bump org.mockito:mockito-core from 5.7.0 to 5.8.0 (#10757)
  Remove abstract
  ...

.git-blame-ignore-revs

@@ -0,0 +1,28 @@
+# Automatic code reformatting
+c5bcad738fe6e8dfcb62442a426c2778241515a1
+
+# net.sf.jabref -> org.jabref
+b2ad6eb279f5def38fa21be12cb5dd4545c1ba1a
+dd385f4ad6dc9251bfdb1c0b75ded402f680b32a
+a6e80311c6376c973b5860658f6e4ace7a3fd1f4
+648a4703e80ac0dbe1ff044f354bc0e332e4064d
+ac08c6a2c55e1600bf5072c0ea2e6aac920b915d
+ec863166cf4f38a1a6bcc80a607fd33299b815aa
+8c61577e4377746fc064db2a136bb68968cd4055
+0ef3228f0c1334ff203d4ea5e698e3ad88cb7089
+ce939b4ef19ca856e7ecac08275cf1ca764207b6
+7f1a8069d03737c202bcb7ce352b3755c6a36f5f
+dbd0cfbc8177ada414e89da038cd014657d48ed3
+bc7ea00c8cc3ec9ec8b1a799b0dd96513bc51404
+9a5cff44aa1e0d4b737296a30b97f7f384c8b885
+bf81b595a77f0f7f254872be6f05a063c44528d8
+277b40c9e79e0158d272de33e24fa7fc06af91bf
+662dd326d212ecfd336a00214e969145ec501c5a
+33f040cfbb16111ada117f858e98d606a6bee4fd
+29fe730f64eeb62ff9de10fcb460a63297e24be6
+
+# This commit should not exist
+185d7345946c29a2a4e2726c912be0c4db4810b9
+# Resulted in this problematic merge commits
+7e1645978b3028df5e65af19f0f819ddfd0f24aa
+a31f396765492ac12eaab228e33eb9d22487403b

.github/workflows/check-links.yml

@@ -29,7 +29,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1.8.0
+        uses: lycheeverse/lychee-action@v1.9.0
         with:
           fail: true
           args: --accept '200,201,202,203,204,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/cleanup-pr.yml

@@ -26,7 +26,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/ssh-action@v1.0.2
+        uses: appleboy/ssh-action@v1.0.3
         with:
           script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
           host: build-upload.jabref.org

.github/workflows/refresh-csl-subtrees.yml

@@ -31,6 +31,11 @@ jobs:
           cd src/main/resources/csl-locales
           git checkout master
           git pull
+      - name: Persist changes
+        run: |
+          git add -f src/main/resources/csl-styles
+          git add -f src/main/resources/csl-locales
+          git diff-index --quiet HEAD || git commit -m 'Update CSL styles'
       - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

.github/workflows/refresh-journal-lists.yml

@@ -37,6 +37,10 @@ jobs:
       - name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
         run: |
           ./gradlew generateJournalListMV
+      - name: Persist changes
+        run: |
+          git add -f buildres/abbrv.jabref.org
+          git diff-index --quiet HEAD || git commit -m 'Update journal abbreviation lists'
       - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

.gitmodules

@@ -1,9 +1,15 @@
-[submodule "buildres/abbrv.jabref.org"]
+[submodule "abbrv.jabref.org"]
   path = buildres/abbrv.jabref.org
   url = https://github.com/JabRef/abbrv.jabref.org.git
-[submodule "buildres/csl-styles"]
+  ignore = all
+  shallow = true
+[submodule "csl-styles"]
   path = src/main/resources/csl-styles
   url = https://github.com/citation-style-language/styles.git
-[submodule "buildres/csl-locales"]
+  ignore = all
+  shallow = true
+[submodule "csl-locales"]
   path = src/main/resources/csl-locales
   url = https://github.com/citation-style-language/locales.git
+  ignore = all
+  shallow = true

CHANGELOG.md

@@ -11,12 +11,21 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
+
 ### Changed
 
+- The "Automatically open folders of attached files" preference default status has been changed to enabled on Windows. [koppor#56](https://github.com/koppor/jabref/issues/56)
+- The Custom export format now uses the custom DOI base URI in the preferences for the `DOICheck`, if activated [forum#4084](https://discourse.jabref.org/t/export-html-disregards-custom-doi-base-uri/4084)
+- The index directories for full text search have now more readable names to increase debugging possibilities using Apache Lucense's Lurk. [#10193](https://github.com/JabRef/jabref/issues/10193)
+- The fulltext search also indexes files ending with .pdf (but do not having an explicit file type set). [#10193](https://github.com/JabRef/jabref/issues/10193)
+- We changed the order of the lists in the "Citation relations" tab. `Cites` are now on the left and `Cited by` on the right [#10572](https://github.com/JabRef/jabref/pull/10752)
+
 ### Fixed
 
 - We fixed an issue where attempting to cancel the importing/generation of an entry from id is ignored. [#10508](https://github.com/JabRef/jabref/issues/10508)
 - We fixed an issue where the preview panel showing the wrong entry (an entry that is not selected in the entry table). [#9172](https://github.com/JabRef/jabref/issues/9172)
+- The last page of a PDF is now indexed by the full text search. [#10193](https://github.com/JabRef/jabref/issues/10193)
 - We fixed an issue where the duplicate check did not take umlauts or other LaTeX-encoded characters into account. [#10744](https://github.com/JabRef/jabref/pull/10744)
 - We fixed the colors of the icon on hover for unset special fields. [#10431](https://github.com/JabRef/jabref/issues/10431)
 

build.gradle

@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.5.4'
+    id 'org.openrewrite.rewrite' version '6.6.3'
 }
 
 // Enable following for debugging
@@ -101,7 +101,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "21"
+    version = "20"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -119,7 +119,7 @@ dependencies {
         exclude group: 'org.junit.jupiter'
     }
 
-    implementation 'org.apache.lucene:lucene-core:9.9.0'
+    implementation 'org.apache.lucene:lucene-core:9.9.1'
     implementation 'org.apache.lucene:lucene-queryparser:9.9.1'
     implementation 'org.apache.lucene:lucene-queries:9.9.0'
     implementation 'org.apache.lucene:lucene-analysis-common:9.9.1'
@@ -184,7 +184,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.2.0'
     implementation 'com.github.Dansoftowner:jSystemThemeDetector:3.8'
 
-    implementation 'org.jsoup:jsoup:1.16.2'
+    implementation 'org.jsoup:jsoup:1.17.2'
     implementation 'com.konghq:unirest-java:3.14.5'
 
     implementation 'org.slf4j:slf4j-api:2.0.9'
@@ -232,7 +232,7 @@ dependencies {
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
-    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.4'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.5'
     testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.5'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
@@ -244,7 +244,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.1'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.1'
 
-    testImplementation 'org.mockito:mockito-core:5.7.0'
+    testImplementation 'org.mockito:mockito-core:5.8.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.2.1'
@@ -433,43 +433,30 @@ test {
         // TODO: Remove this as soon as ArchUnit is modularized
         runOnClasspath = true
     }
-
-    testLogging {
-        // set options for log level LIFECYCLE
-        // for debugging tests: add "STANDARD_OUT", "STANDARD_ERROR"
-        events = ["FAILED"]
-        exceptionFormat "full"
-    }
 }
 
 testlogger {
-    theme 'standard-parallel'
+    // See https://github.com/radarsh/gradle-test-logger-plugin#configuration for configuration options
+
+    theme 'standard'
+
     showPassed false
     showSkipped false
+
+    showCauses false
+    showStackTraces false
 }
 
 tasks.register('databaseTest', Test) {
     useJUnitPlatform {
         includeTags 'DatabaseTest'
     }
-
-    testLogging {
-        // set options for log level LIFECYCLE
-        events = ["FAILED"]
-        exceptionFormat "full"
-    }
 }
 
 tasks.register('fetcherTest', Test) {
     useJUnitPlatform {
         includeTags 'FetcherTest'
     }
-
-    testLogging {
-        // set options for log level LIFECYCLE
-        events = ["FAILED"]
-        exceptionFormat "full"
-    }
 }
 
 tasks.register('guiTest', Test) {

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-89-run-with-intellij.md

@@ -18,10 +18,12 @@ Due to [IDEA-119280](https://youtrack.jetbrains.com/issue/IDEA-119280), it is a
 6. Open the project view (<kbd>Alt</kbd>+<kbd>1</kbd> , on mac <kbd>cmd><kbd>+<kbd>1</kbd>)
 7. Copy all build resources to the folder of the build classes
    1. Navigate to the folder `build/resoruces/main`
-   2. Select all folders below (`bst`, `csl-locales`, ...)
-   3. Press <kbd>Ctrl</kbd>+<kbd>C</kbd> to mark them for copying
-   4. Select the folder `out/production/classes`
-   5. Press <kbd>Ctrl</kbd>+<kbd>V</kbd> to start the copy process
+   1. Right click -> "Open In" -> "Explorer (Finder on macOS)"
+   1. Navigate into directory "main"
+   1. Select the folder `out/production/classes`
+   1. Right click -> "Open In" -> "Explorer (Finder on macOS)"
+   1. Navigate into directory "classes"
+   1. Now you have two Explorer windows opened. Copy all files and directories from the first one to the second one.
 8. Locate the class `Launcher` (e.g., by <kbd>ctrl</kbd>+<kbd>N</kbd> and then typing `Launcher`). Press <kbd>Enter</kbd> to jump to that class.
    <figure>
      <img src="intellij-search-for-launcher.png" alt="IntelliJ search for class “Launcher”">

src/main/java/org/jabref/gui/JabRefExecutorService.java

@@ -13,6 +13,8 @@
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
+import org.jabref.logic.pdf.search.PdfIndexerManager;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -146,6 +148,8 @@ public void shutdownEverything() {
         gracefullyShutdown(this.executorService);
         gracefullyShutdown(this.lowPriorityExecutorService);
 
+        PdfIndexerManager.shutdownAllIndexers();
+
         timer.cancel();
     }