Merge branch 'main' into remove-mainapplication-layer

CHANGELOG.md

@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new group icon column to the main table showing the icons of the entry's groups. [#10801](https://github.com/JabRef/jabref/pull/10801)
 - We added ability to jump to an entry in the command line using `-j CITATIONKEY`. [koppor#540](https://github.com/koppor/jabref/issues/540)
 - We added a new boolean to the style files for Openoffice/Libreoffice integration to switch between ZERO_WIDTH_SPACE (default) and no space. [#10843](https://github.com/JabRef/jabref/pull/10843)
+- We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 
 ### Changed
 

build.gradle

@@ -9,7 +9,7 @@ plugins {
 
     id 'me.champeau.jmh' version '0.7.2'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.12'
+    id 'org.javamodularity.moduleplugin' version '1.8.13'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
@@ -122,7 +122,7 @@ dependencies {
     implementation 'org.apache.lucene:lucene-core:9.9.2'
     implementation 'org.apache.lucene:lucene-queryparser:9.9.2'
     implementation 'org.apache.lucene:lucene-queries:9.9.1'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.9.1'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.9.2'
     implementation 'org.apache.lucene:lucene-highlighter:9.9.2'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
@@ -176,7 +176,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.92.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.97.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -242,7 +242,7 @@ dependencies {
 
     testImplementation 'io.github.classgraph:classgraph:4.8.165'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.1'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 
     testImplementation 'org.mockito:mockito-core:5.10.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
@@ -258,7 +258,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.6.3"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.6.4"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

docs/code-howtos/index.md

@@ -25,7 +25,7 @@ Example: [NormalizePagesFormatter](https://github.com/JabRef/jabref/blob/master/
 
 ## Drag and Drop
 
-Drag and Drop makes usage of the Dragboard. For JavaFX the following [tutorial](https://docs.oracle.com/javafx/2/drag\_drop/jfxpub-drag\_drop.htm) is helpful. Note that the data has to be serializable which is put on the dragboard. For drag and drop of Bib-entries between the maintable and the groups panel, a custom Dragboard is used, `CustomLocalDragboard` which is a generic alternative to the system one.
+Drag and Drop makes usage of the Dragboard. For JavaFX the following [tutorial](https://docs.oracle.com/javafx/2/drag_drop/jfxpub-drag_drop.htm) is helpful. Note that the data has to be serializable which is put on the dragboard. For drag and drop of Bib-entries between the maintable and the groups panel, a custom Dragboard is used, `CustomLocalDragboard` which is a generic alternative to the system one.
 
 For accessing or putting data into the Clipboard use the `ClipboardManager`.
 

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

@@ -44,6 +44,7 @@
 import org.jabref.gui.integrity.IntegrityCheckAction;
 import org.jabref.gui.journals.AbbreviateAction;
 import org.jabref.gui.libraryproperties.LibraryPropertiesAction;
+import org.jabref.gui.linkedfile.RedownloadMissingFilesAction;
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.preferences.ShowPreferencesAction;
 import org.jabref.gui.preview.CopyCitationAction;
@@ -287,7 +288,11 @@ private void createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.REBUILD_FULLTEXT_SEARCH_INDEX, new RebuildFulltextSearchIndexAction(stateManager, frame::getCurrentLibraryTab, dialogService, preferencesService.getFilePreferences(), taskExecutor))
+                factory.createMenuItem(StandardActions.REBUILD_FULLTEXT_SEARCH_INDEX, new RebuildFulltextSearchIndexAction(stateManager, frame::getCurrentLibraryTab, dialogService, preferencesService.getFilePreferences(), taskExecutor)),
+
+                new SeparatorMenuItem(),
+
+                factory.createMenuItem(StandardActions.REDOWNLOAD_MISSING_FILES, new RedownloadMissingFilesAction(stateManager, dialogService, preferencesService.getFilePreferences(), taskExecutor))
         );
         SidePaneType webSearchPane = SidePaneType.WEB_SEARCH;
         SidePaneType groupsPane = SidePaneType.GROUPS;

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -30,6 +30,7 @@ public enum StandardActions implements Action {
     SEND_AS_EMAIL(Localization.lang("As Email")),
     SEND_TO_KINDLE(Localization.lang("To Kindle")),
     REBUILD_FULLTEXT_SEARCH_INDEX(Localization.lang("Rebuild fulltext search index"), IconTheme.JabRefIcons.FILE),
+    REDOWNLOAD_MISSING_FILES(Localization.lang("Redownload missing files"), IconTheme.JabRefIcons.DOWNLOAD),
     OPEN_EXTERNAL_FILE(Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
     OPEN_URL(Localization.lang("Open URL or DOI"), IconTheme.JabRefIcons.WWW, KeyBinding.OPEN_URL_OR_DOI),
     SEARCH_SHORTSCIENCE(Localization.lang("Search ShortScience")),
@@ -149,6 +150,7 @@ public enum StandardActions implements Action {
 
     EDIT_FILE_LINK(Localization.lang("Edit"), IconTheme.JabRefIcons.EDIT, KeyBinding.EDIT_ENTRY),
     DOWNLOAD_FILE(Localization.lang("Download file"), IconTheme.JabRefIcons.DOWNLOAD_FILE),
+    REDOWNLOAD_FILE(Localization.lang("Redownload file"), IconTheme.JabRefIcons.DOWNLOAD_FILE),
     RENAME_FILE_TO_PATTERN(Localization.lang("Rename file to defined pattern"), IconTheme.JabRefIcons.AUTO_RENAME),
     RENAME_FILE_TO_NAME(Localization.lang("Rename file to a given name"), IconTheme.JabRefIcons.RENAME, KeyBinding.REPLACE_STRING),
     MOVE_FILE_TO_FOLDER(Localization.lang("Move file to file directory"), IconTheme.JabRefIcons.MOVE_TO_FOLDER),