From 18f87e919412995bffac314cc6dd8b0b1cdf3d79 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 13 Sep 2026 23:59:19 +0200
Subject: [PATCH 01/13] Persist group membership in sidecars and make file
 renames opt-in

Explicit group membership was lost across restarts because the `groups` field had no
Hayagriva key. Sidecar renames now follow "Auto rename files if entry changes", with a
library-level override in the General properties tab that also applies to .bib libraries.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 CHANGELOG.md                                  |  1 +
 docs/requirements/directory-library.md        | 10 +++++---
 .../AutoRenameFileOnEntryChange.java          |  4 ++-
 .../actions/OpenDirectoryLibraryAction.java   |  8 ++++--
 .../general/GeneralPropertiesView.java        | 15 +++++++++++
 .../general/GeneralPropertiesViewModel.java   |  7 ++++++
 .../general/GeneralProperties.fxml            |  4 +++
 .../directorylibrary/SidecarWriteBack.java    |  2 +-
 .../logic/exporter/MetaDataSerializer.java    |  2 ++
 .../importer/fileformat/HayagrivaMapping.java |  8 +++---
 .../logic/importer/util/MetaDataParser.java   |  2 ++
 .../org/jabref/model/metadata/MetaData.java   | 25 ++++++++++++++++---
 .../main/resources/l10n/JabRef_en.properties  |  3 +++
 .../exporter/HayagrivaEntryWriterTest.java    | 22 ++++++++++++++++
 .../exporter/MetaDataSerializerTest.java      |  7 ++++++
 .../importer/util/MetaDataParserTest.java     |  8 ++++++
 16 files changed, 114 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55ecba5a5f95..61af1aba8f03 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -86,6 +86,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added OCR language selection to the OCR preferences, allowing users to configure which Tesseract languages to use. [#16618](https://github.com/JabRef/jabref/issues/16618)
 - We added a fetcher for the Bielefeld Academic Search Engine (BASE). [#15016](https://github.com/JabRef/jabref/issues/15016)
 - We added a Git section to the library properties for automatic commit, pull and push. [#12630](https://github.com/JabRef/jabref/issues/12630)
+- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#17111](https://github.com/JabRef/jabref/pull/17111)
 - We added connection URL pasting to the shared database login dialog. [#16800](https://github.com/JabRef/jabref/pull/16800)
 - We added a Dnb Fetcher that uses SRU interface and wired to ISBN Fetcher. [#17070](https://github.com/JabRef/jabref/pull/17070)
 - We added read-only access to shared SQL libraries in `jabkit`: every input file argument accepts a PostgreSQL URL. [#12948](https://github.com/JabRef/jabref/issues/12948)
diff --git a/docs/requirements/directory-library.md b/docs/requirements/directory-library.md
index 92a86318b104..1c5066aa3e0a 100644
--- a/docs/requirements/directory-library.md
+++ b/docs/requirements/directory-library.md
@@ -82,11 +82,13 @@ entries or subgroups can be added to them, they cannot be dragged or edited.
 Needs: impl
 
 ## The sidecar and its PDF follow the configured filename pattern
-`req~directory-library.pattern-rename~1`
+`req~directory-library.pattern-rename~2`
 
-When write-back touches a single-entry sidecar, the sidecar and its equally named PDF are
-renamed together to the base name the configured filename pattern (Linked files preferences)
-generates for the entry, keeping the pair in sync. Multi-entry files have no single generating
+When write-back touches a single-entry sidecar and auto-renaming is enabled, the sidecar and
+its equally named PDF are renamed together to the base name the configured filename pattern
+(Linked files preferences) generates for the entry, keeping the pair in sync. Auto-renaming
+follows the global "Auto rename files if entry changes" preference unless the library
+properties override it (General tab; the same override applies to `.bib` libraries). Multi-entry files have no single generating
 entry and keep their name; occupied target names and pattern failures leave the current name
 untouched. Entry file links and the catalog follow the rename; the watcher does not re-import
 the renamed files.
diff --git a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
index 98af6a04f795..33752c6685b1 100644
--- a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
+++ b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
@@ -14,17 +14,19 @@
 public class AutoRenameFileOnEntryChange {
     private static final Logger LOGGER = LoggerFactory.getLogger(AutoRenameFileOnEntryChange.class);
 
+    private final BibDatabaseContext bibDatabaseContext;
     private final FilePreferences filePreferences;
     private final RenamePdfCleanup renamePdfCleanup;
 
     public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
+        this.bibDatabaseContext = bibDatabaseContext;
         this.filePreferences = filePreferences;
         renamePdfCleanup = new RenamePdfCleanup(false, () -> bibDatabaseContext, filePreferences);
     }
 
     @Subscribe
     public void listen(FieldChangedEvent event) {
-        if (!filePreferences.shouldAutoRenameFilesOnChange()
+        if (!bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(filePreferences.shouldAutoRenameFilesOnChange())
                 || filePreferences.getFileNamePattern().isEmpty()
                 || filePreferences.getFileNamePattern() == null) {
             return;
diff --git a/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java b/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
index aa4eaea0ff1d..7165b2e50604 100644
--- a/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
+++ b/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
@@ -160,8 +160,12 @@ private void showLibraryTab(DirectoryLibraryScanner.ScanResult scanResult, PdfEn
         libraryTab.updateTabTitle(false);
 
         BibDatabaseContext databaseContext = scanResult.databaseContext();
-        Function<BibEntry, Optional<String>> fileNameGenerator = entry -> FileUtil.createFileNameFromPattern(
-                databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileNamePattern());
+        // Evaluated per write, so a changed preference (global or library) takes effect immediately
+        // [impl->req~directory-library.pattern-rename~2]
+        Function<BibEntry, Optional<String>> fileNameGenerator = entry ->
+                databaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(preferences.getFilePreferences().shouldAutoRenameFilesOnChange())
+                ? FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileNamePattern())
+                : Optional.empty();
         GuiGitConflictResolverStrategy conflictResolver = new GuiGitConflictResolverStrategy(
                 new GitConflictResolverDialog(dialogService, preferences, stateManager));
         DirectoryLibrarySynchronizer synchronizer = new DirectoryLibrarySynchronizer(
diff --git a/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java b/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java
index e745030452ff..2d22941b6b21 100644
--- a/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java
+++ b/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java
@@ -2,9 +2,11 @@
 
 import java.nio.charset.Charset;
 import java.nio.file.Path;
+import java.util.Optional;
 import java.util.function.UnaryOperator;
 
 import javafx.application.Platform;
+import javafx.collections.FXCollections;
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
 import javafx.scene.control.ComboBox;
@@ -37,6 +39,7 @@ public class GeneralPropertiesView extends AbstractPropertiesTabView<GeneralProp
     @FXML private TextField userSpecificFileDirectory;
     @FXML private TextField latexFileDirectory;
     @FXML private TextField keywordSeparator;
+    @FXML private ComboBox<Optional<Boolean>> autoRenameFilesOnChange;
     @FXML private Button libSpecificFileDirSwitchId;
     @FXML private Button userSpecificFileDirSwitchId;
     @FXML private Button laTexSpecificFileDirSwitchId;
@@ -101,6 +104,14 @@ public void initialize() {
                 change -> change.getControlNewText().length() <= 1 ? change : null;
         keywordSeparator.setTextFormatter(new TextFormatter<>(singleCharacterFilter));
 
+        boolean globalAutoRename = preferences.getFilePreferences().shouldAutoRenameFilesOnChange();
+        new ViewModelListCellFactory<Optional<Boolean>>()
+                .withText(choice -> choice.map(GeneralPropertiesView::yesOrNo)
+                                          .orElse(Localization.lang("Use global preference (%0)", yesOrNo(globalAutoRename))))
+                .install(autoRenameFilesOnChange);
+        autoRenameFilesOnChange.setItems(FXCollections.observableArrayList(Optional.empty(), Optional.of(true), Optional.of(false)));
+        autoRenameFilesOnChange.valueProperty().bindBidirectional(viewModel.autoRenameFilesOnChangeProperty());
+
         userSpecificFileDirectoryTooltip.setText(Localization.lang("User-specific file directory: %0", preferences.getFilePreferences().getUserAndHost()));
         userSpecificFileDirectory.setTooltip(userSpecificFileDirectoryTooltip);
 
@@ -179,4 +190,8 @@ void userSpecificFileDirPathSwitch() {
     void laTexSpecificFileDirPathSwitch() {
         viewModel.togglePath(viewModel.laTexFileDirectoryProperty());
     }
+
+    private static String yesOrNo(boolean value) {
+        return value ? Localization.lang("Yes") : Localization.lang("No");
+    }
 }
diff --git a/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java b/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java
index 31e42d327ff4..05ed0a05d4da 100644
--- a/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java
+++ b/jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java
@@ -47,6 +47,7 @@ public class GeneralPropertiesViewModel implements PropertiesTabViewModel {
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty laTexFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty keywordSeparatorProperty = new SimpleStringProperty("");
+    private final ObjectProperty<Optional<Boolean>> autoRenameFilesOnChangeProperty = new SimpleObjectProperty<>(Optional.empty());
 
     private final Validator librarySpecificFileDirectoryValidator;
     private final Validator userSpecificFileDirectoryValidator;
@@ -91,6 +92,7 @@ public void setValues(MetaData metaData) {
         userSpecificFileDirectoryProperty.setValue(metaData.getUserFileDirectory(preferences.getFilePreferences().getUserAndHost()).orElse("").trim());
         laTexFileDirectoryProperty.setValue(metaData.getLatexFileDirectory(preferences.getFilePreferences().getUserAndHost()).map(Path::toString).orElse(""));
         keywordSeparatorProperty.setValue(metaData.getKeywordSeparator().map(Object::toString).orElse(""));
+        autoRenameFilesOnChangeProperty.setValue(metaData.getAutoRenameFilesOnChange());
     }
 
     @Override
@@ -120,6 +122,7 @@ public void storeSettings(MetaData metaData) {
         }
 
         storeKeywordSeparator(metaData);
+        autoRenameFilesOnChangeProperty.getValue().ifPresentOrElse(metaData::setAutoRenameFilesOnChange, metaData::clearAutoRenameFilesOnChange);
     }
 
     /// The separator and the group definitions the migration rewrites are both metadata, so the
@@ -225,6 +228,10 @@ public StringProperty keywordSeparatorProperty() {
         return this.keywordSeparatorProperty;
     }
 
+    public ObjectProperty<Optional<Boolean>> autoRenameFilesOnChangeProperty() {
+        return this.autoRenameFilesOnChangeProperty;
+    }
+
     private Path getBrowseDirectory(String configuredDir) {
         Optional<Path> libPath = this.databaseContext.getDatabasePath();
         Path workingDir = preferences.getFilePreferences().getWorkingDirectory();
diff --git a/jabgui/src/main/resources/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml b/jabgui/src/main/resources/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml
index ab0665cee773..390a93dc31a5 100644
--- a/jabgui/src/main/resources/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml
+++ b/jabgui/src/main/resources/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml
@@ -135,6 +135,10 @@
                GridPane.columnIndex="0" GridPane.rowIndex="7"/>
         <TextField fx:id="keywordSeparator" prefWidth="50.0" maxWidth="50.0"
                    GridPane.columnIndex="1" GridPane.rowIndex="7"/>
+        <Label text="%Auto rename files if entry changes"
+               GridPane.columnIndex="0" GridPane.rowIndex="8"/>
+        <ComboBox fx:id="autoRenameFilesOnChange" prefWidth="150.0"
+                  GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" GridPane.rowIndex="8"/>
 
     </GridPane>
 </fx:root>
diff --git a/jablib/src/main/java/org/jabref/logic/directorylibrary/SidecarWriteBack.java b/jablib/src/main/java/org/jabref/logic/directorylibrary/SidecarWriteBack.java
index 88968c7dcd6d..636eb2dbfd80 100644
--- a/jablib/src/main/java/org/jabref/logic/directorylibrary/SidecarWriteBack.java
+++ b/jablib/src/main/java/org/jabref/logic/directorylibrary/SidecarWriteBack.java
@@ -43,7 +43,7 @@
 /// The debounce, retry, and reporting of pending writes live in [PendingWrites]; this class
 /// only knows how to write one file. Callers hold the synchronizer's monitor.
 // [impl->req~directory-library.write-back~2]
-// [impl->req~directory-library.pattern-rename~1]
+// [impl->req~directory-library.pattern-rename~2]
 @NullMarked
 class SidecarWriteBack {
 
diff --git a/jablib/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java b/jablib/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
index fdc6a8910a36..7f57b7aedac7 100644
--- a/jablib/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
+++ b/jablib/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
@@ -54,6 +54,8 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
         if (metaData.isGitAutoPush()) {
             stringyMetaData.put(MetaData.GIT_AUTO_PUSH, List.of("true"));
         }
+        metaData.getAutoRenameFilesOnChange().ifPresent(
+                autoRename -> stringyMetaData.put(MetaData.AUTO_RENAME_FILES_ON_CHANGE, List.of(autoRename.toString())));
         stringyMetaData.putAll(serializeCiteKeyPatterns(metaData, globalCiteKeyPatterns));
         metaData.getMode().ifPresent(
                 mode -> stringyMetaData.put(MetaData.DATABASE_TYPE, List.of(mode.getAsString())));
diff --git a/jablib/src/main/java/org/jabref/logic/importer/fileformat/HayagrivaMapping.java b/jablib/src/main/java/org/jabref/logic/importer/fileformat/HayagrivaMapping.java
index dc1d658d03c7..8adf1a9a5c91 100644
--- a/jablib/src/main/java/org/jabref/logic/importer/fileformat/HayagrivaMapping.java
+++ b/jablib/src/main/java/org/jabref/logic/importer/fileformat/HayagrivaMapping.java
@@ -59,9 +59,10 @@ public final class HayagrivaMapping {
     /// order. `title` and `url` are "formattable strings" (scalar or map with a `value` key) and
     /// are handled separately, as are the person lists and `serial-number`.
     ///
-    /// `comment` (like the per-user `comment-<name>` keys, see [#USER_COMMENT_PREFIX]) is not
-    /// part of the Hayagriva specification but a JabRef extension key: the Hayagriva parser
-    /// silently ignores keys it does not know, so such files stay loadable by Typst.
+    /// `comment` (like the per-user `comment-<name>` keys, see [#USER_COMMENT_PREFIX]) and
+    /// `groups` (explicit group membership) are not part of the Hayagriva specification but
+    /// JabRef extension keys: the Hayagriva parser silently ignores keys it does not know, so
+    /// such files stay loadable by Typst.
     public static final SequencedMap<String, Field> SCALAR_FIELDS;
 
     /// `serial-number` sub-keys with a dedicated BibEntry field. `arxiv` is handled separately
@@ -111,6 +112,7 @@ public final class HayagrivaMapping {
         scalars.put("note", StandardField.NOTE);
         scalars.put("abstract", StandardField.ABSTRACT);
         scalars.put("comment", StandardField.COMMENT);
+        scalars.put("groups", StandardField.GROUPS);
         SCALAR_FIELDS = Collections.unmodifiableSequencedMap(scalars);
 
         SequencedMap<String, Field> serialNumbers = new LinkedHashMap<>();
diff --git a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
index 1356e55f1b67..ea9be3d99965 100644
--- a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
+++ b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
@@ -161,6 +161,8 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
                 metaData.setGitAutoCommit(Boolean.parseBoolean(getSingleItem(values)));
             } else if (MetaData.GIT_AUTO_PUSH.equals(entry.getKey())) {
                 metaData.setGitAutoPush(Boolean.parseBoolean(getSingleItem(values)));
+            } else if (MetaData.AUTO_RENAME_FILES_ON_CHANGE.equals(entry.getKey())) {
+                metaData.setAutoRenameFilesOnChange(Boolean.parseBoolean(getSingleItem(values)));
             } else if (MetaData.SAVE_ORDER_CONFIG.equals(entry.getKey())) {
                 metaData.setSaveOrder(SaveOrder.parse(values));
             } else if (MetaData.GROUPSTREE.equals(entry.getKey()) || MetaData.GROUPSTREE_LEGACY.equals(entry.getKey())) {
diff --git a/jablib/src/main/java/org/jabref/model/metadata/MetaData.java b/jablib/src/main/java/org/jabref/model/metadata/MetaData.java
index bf3ee68b3469..35da53eacc4f 100644
--- a/jablib/src/main/java/org/jabref/model/metadata/MetaData.java
+++ b/jablib/src/main/java/org/jabref/model/metadata/MetaData.java
@@ -68,6 +68,7 @@ public class MetaData {
     public static final String GIT_AUTO_PULL = "gitAutoPull";
     public static final String GIT_AUTO_COMMIT = "gitAutoCommit";
     public static final String GIT_AUTO_PUSH = "gitAutoPush";
+    public static final String AUTO_RENAME_FILES_ON_CHANGE = "autoRenameFilesOnChange";
 
     private final EventBus eventBus = new EventBus();
     private final Map<EntryType, String> citeKeyPatterns = new HashMap<>(); // <BibType, Pattern>
@@ -100,6 +101,8 @@ public class MetaData {
     private boolean containsSearchGroups;
 
     private boolean gitAutoPull;
+    /// Library override of the global "auto rename files if entry changes" preference; absent = use the global one
+    @Nullable private Boolean autoRenameFilesOnChange;
     private boolean gitAutoCommit;
     private boolean gitAutoPush;
 
@@ -183,6 +186,20 @@ public boolean isGitAutoPull() {
         return gitAutoPull;
     }
 
+    public Optional<Boolean> getAutoRenameFilesOnChange() {
+        return Optional.ofNullable(autoRenameFilesOnChange);
+    }
+
+    public void setAutoRenameFilesOnChange(boolean autoRenameFilesOnChange) {
+        this.autoRenameFilesOnChange = autoRenameFilesOnChange;
+        postChange();
+    }
+
+    public void clearAutoRenameFilesOnChange() {
+        autoRenameFilesOnChange = null;
+        postChange();
+    }
+
     public void setGitAutoPull(boolean gitAutoPull) {
         this.gitAutoPull = gitAutoPull;
         postChange();
@@ -463,6 +480,7 @@ public void overwriteWith(@NonNull MetaData other, MetaDataChangeSource source)
         gitAutoPull = other.gitAutoPull;
         gitAutoCommit = other.gitAutoCommit;
         gitAutoPush = other.gitAutoPush;
+        autoRenameFilesOnChange = other.autoRenameFilesOnChange;
 
         other.getGroups()
              .map(GroupTreeNode::copySubtree)
@@ -579,18 +597,19 @@ public boolean equals(Object o) {
                 && Objects.equals(aiLibraryId, that.aiLibraryId)
                 && (gitAutoPull == that.gitAutoPull)
                 && (gitAutoCommit == that.gitAutoCommit)
-                && (gitAutoPush == that.gitAutoPush);
+                && (gitAutoPush == that.gitAutoPush)
+                && Objects.equals(autoRenameFilesOnChange, that.autoRenameFilesOnChange);
     }
 
     @Override
     public int hashCode() {
         return Objects.hash(isProtected, groupsRoot.getValue(), encoding, encodingExplicitlySupplied, saveOrder, citeKeyPatterns, userFileDirectory,
-                latexFileDirectory, defaultCiteKeyPattern, saveActions, mode, keywordSeparator, librarySpecificFileDirectory, contentSelectors, versionDBStructure, aiLibraryId, gitAutoPull, gitAutoCommit, gitAutoPush);
+                latexFileDirectory, defaultCiteKeyPattern, saveActions, mode, keywordSeparator, librarySpecificFileDirectory, contentSelectors, versionDBStructure, aiLibraryId, gitAutoPull, gitAutoCommit, gitAutoPush, autoRenameFilesOnChange);
     }
 
     @Override
     public String toString() {
-        return "MetaData [citeKeyPatterns=" + citeKeyPatterns + ", userFileDirectory=" + userFileDirectory + ", laTexFileDirectory=" + latexFileDirectory + ", groupsRoot=" + groupsRoot + ", encoding=" + encoding + ", saveOrderConfig=" + saveOrder + ", defaultCiteKeyPattern=" + defaultCiteKeyPattern + ", saveActions=" + saveActions + ", mode=" + mode + ", keywordSeparator=" + keywordSeparator + ", isProtected=" + isProtected + ", librarySpecificFileDirectory=" + librarySpecificFileDirectory + ", contentSelectors=" + contentSelectors + ", encodingExplicitlySupplied=" + encodingExplicitlySupplied + ", VersionDBStructure=" + versionDBStructure + ", aiLibraryId=" + aiLibraryId + ", gitAutoPull=" + gitAutoPull + ", gitAutoCommit=" + gitAutoCommit + ", gitAutoPush=" + gitAutoPush + "]";
+        return "MetaData [citeKeyPatterns=" + citeKeyPatterns + ", userFileDirectory=" + userFileDirectory + ", laTexFileDirectory=" + latexFileDirectory + ", groupsRoot=" + groupsRoot + ", encoding=" + encoding + ", saveOrderConfig=" + saveOrder + ", defaultCiteKeyPattern=" + defaultCiteKeyPattern + ", saveActions=" + saveActions + ", mode=" + mode + ", keywordSeparator=" + keywordSeparator + ", isProtected=" + isProtected + ", librarySpecificFileDirectory=" + librarySpecificFileDirectory + ", contentSelectors=" + contentSelectors + ", encodingExplicitlySupplied=" + encodingExplicitlySupplied + ", VersionDBStructure=" + versionDBStructure + ", aiLibraryId=" + aiLibraryId + ", gitAutoPull=" + gitAutoPull + ", gitAutoCommit=" + gitAutoCommit + ", gitAutoPush=" + gitAutoPush + ", autoRenameFilesOnChange=" + autoRenameFilesOnChange + "]";
     }
 
     public Optional<Path> getBlgFilePath(String user) {
diff --git a/jablib/src/main/resources/l10n/JabRef_en.properties b/jablib/src/main/resources/l10n/JabRef_en.properties
index de7869ced729..75cdf0d6b46b 100644
--- a/jablib/src/main/resources/l10n/JabRef_en.properties
+++ b/jablib/src/main/resources/l10n/JabRef_en.properties
@@ -3741,3 +3741,6 @@ Move\ group=Move group
 Sort\ subgroups=Sort subgroups
 Change\ string\ constants=Change string constants
 Founded\ by\ Morten\ O.\ Alver\ and\ Nizar\ Batada.=Founded by Morten O. Alver and Nizar Batada.
+Use\ global\ preference\ (%0)=Use global preference (%0)
+Yes=Yes
+No=No
diff --git a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
index cbe922b9f225..e180562e5d82 100644
--- a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
+++ b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
@@ -2,6 +2,7 @@
 
 import java.net.URISyntaxException;
 import java.nio.file.Path;
+import java.util.Optional;
 
 import org.jabref.logic.importer.fileformat.HayagrivaMapping;
 import org.jabref.model.entry.BibEntry;
@@ -244,6 +245,27 @@ void mergeWritesCommentAndPerUserComment() {
                 """), node);
     }
 
+    @Test
+    void mergeWritesGroupMembershipAndReadsItBack() {
+        ObjectNode node = parseEntryNode("""
+                key:
+                    type: article
+                    title: Some Title
+                """);
+        BibEntry entry = HayagrivaMapping.toBibEntry("key", node);
+        entry.setField(StandardField.GROUPS, "Reading list, Favorites");
+
+        writer.mergeIntoNode(entry, node);
+
+        assertEquals(parseEntryNode("""
+                key:
+                    type: article
+                    title: Some Title
+                    groups: Reading list, Favorites
+                """), node);
+        assertEquals(Optional.of("Reading list, Favorites"), HayagrivaMapping.toBibEntry("key", node).getField(StandardField.GROUPS));
+    }
+
     @Test
     void mergeRemovesClearedComments() {
         ObjectNode node = parseEntryNode("""
diff --git a/jablib/src/test/java/org/jabref/logic/exporter/MetaDataSerializerTest.java b/jablib/src/test/java/org/jabref/logic/exporter/MetaDataSerializerTest.java
index d4befc95c427..1acbfd471332 100644
--- a/jablib/src/test/java/org/jabref/logic/exporter/MetaDataSerializerTest.java
+++ b/jablib/src/test/java/org/jabref/logic/exporter/MetaDataSerializerTest.java
@@ -70,6 +70,13 @@ void serializeKeywordSeparator() {
         assertEquals(Map.of("keywordSeparator", "\\;;"), MetaDataSerializer.getSerializedStringMap(metaData, pattern));
     }
 
+    @Test
+    void serializeAutoRenameFilesOnChangeOverride() {
+        metaData.setAutoRenameFilesOnChange(false);
+
+        assertEquals(Map.of("autoRenameFilesOnChange", "false;"), MetaDataSerializer.getSerializedStringMap(metaData, pattern));
+    }
+
     @Test
     void serializeSingleSaveAction() {
         FieldFormatterCleanupActions saveActions = new FieldFormatterCleanupActions(true,
diff --git a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
index 878281fe514e..6b15204ca446 100644
--- a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
+++ b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
@@ -106,6 +106,14 @@ void parsesAiLibraryId() throws ParseException {
         assertEquals(Optional.of("test-ai-library-id"), parsed.getAiLibraryId());
     }
 
+    @Test
+    void parsesAutoRenameFilesOnChangeOverride() throws ParseException {
+        MetaDataParser parser = new MetaDataParser(new DummyFileUpdateMonitor());
+        MetaData parsed = parser.parse(Map.of(MetaData.AUTO_RENAME_FILES_ON_CHANGE, "false;"), ',', "userAndHost");
+
+        assertEquals(Optional.of(false), parsed.getAutoRenameFilesOnChange());
+    }
+
     @Test
     void parsesKeywordSeparator() throws ParseException {
         MetaDataParser parser = new MetaDataParser(new DummyFileUpdateMonitor());

From 37b00f16b504cb4e67a56381bc848171baa700f4 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:01:16 +0200
Subject: [PATCH 02/13] Cover group membership across a directory-library
 restart

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../DirectoryLibrarySynchronizerTest.java              | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
index 3e7a9b2d8b3e..bd5eb0116653 100644
--- a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
+++ b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
@@ -1004,11 +1004,15 @@ void userGroupsFromMirrorMetadataAreRestoredAtOpen() throws IOException, Interru
         openLibrary();
         synchronizer.doInitializeMirror();
         synchronizer.flush();
-        context.getMetaData().getGroups().orElseThrow()
-               .addSubgroup(new ExplicitGroup("My group", GroupHierarchyType.INDEPENDENT, ','));
+        ExplicitGroup group = new ExplicitGroup("My group", GroupHierarchyType.INDEPENDENT, ',');
+        context.getMetaData().getGroups().orElseThrow().addSubgroup(group);
         // Delivered by the context's change filter in the application
         synchronizer.listen(new GroupUpdatedEvent(context.getMetaData()));
+        BibEntry entry = entries().getFirst();
+        group.add(entry);
+        synchronizer.handleLocalChange(entry);
         synchronizer.awaitPendingEvents();
+        synchronizer.flush();
         synchronizer.shutdown();
 
         openLibrary();
@@ -1019,6 +1023,8 @@ void userGroupsFromMirrorMetadataAreRestoredAtOpen() throws IOException, Interru
         assertEquals(List.of(DirectoryStructureGroup.class, ExplicitGroup.class),
                 children.stream().map(child -> child.getGroup().getClass()).toList());
         assertEquals("My group", children.getLast().getName());
+        // Membership lives in the entry's groups field and must survive the sidecar round trip
+        assertTrue(children.getLast().getGroup().contains(entries().getFirst()));
     }
 
     /// [utest->req~directory-library.convert~1]

From ebb02010493d43872b5cb13caded486ce1227f5c Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:01:30 +0200
Subject: [PATCH 03/13] Link the changelog entry to its pull request

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 61af1aba8f03..c80c2041dba6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -86,7 +86,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added OCR language selection to the OCR preferences, allowing users to configure which Tesseract languages to use. [#16618](https://github.com/JabRef/jabref/issues/16618)
 - We added a fetcher for the Bielefeld Academic Search Engine (BASE). [#15016](https://github.com/JabRef/jabref/issues/15016)
 - We added a Git section to the library properties for automatic commit, pull and push. [#12630](https://github.com/JabRef/jabref/issues/12630)
-- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#17111](https://github.com/JabRef/jabref/pull/17111)
+- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#769](https://github.com/JabRef/jabref-koppor/pull/769)
 - We added connection URL pasting to the shared database login dialog. [#16800](https://github.com/JabRef/jabref/pull/16800)
 - We added a Dnb Fetcher that uses SRU interface and wired to ISBN Fetcher. [#17070](https://github.com/JabRef/jabref/pull/17070)
 - We added read-only access to shared SQL libraries in `jabkit`: every input file argument accepts a PostgreSQL URL. [#12948](https://github.com/JabRef/jabref/issues/12948)

From 030485f5863a194b53b3fbfc48fee39437968dc1 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:07:26 +0200
Subject: [PATCH 04/13] Share the rename precedence, reject malformed
 overrides, tighten tests

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../AutoRenameFileOnEntryChange.java          |  7 ++++-
 .../actions/OpenDirectoryLibraryAction.java   |  3 +-
 .../AutoRenameFileOnEntryChangeTest.java      | 29 ++++++++++++++++++-
 .../logic/importer/util/MetaDataParser.java   |  8 ++++-
 .../DirectoryLibrarySynchronizerTest.java     |  2 +-
 .../exporter/HayagrivaEntryWriterTest.java    |  4 +--
 .../importer/util/MetaDataParserTest.java     |  8 +++++
 7 files changed, 54 insertions(+), 7 deletions(-)

diff --git a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
index 33752c6685b1..d414f7ab7d46 100644
--- a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
+++ b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
@@ -24,9 +24,14 @@ public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePr
         renamePdfCleanup = new RenamePdfCleanup(false, () -> bibDatabaseContext, filePreferences);
     }
 
+    /// The library properties override the global preference when set (`MetaData#getAutoRenameFilesOnChange`).
+    public static boolean isEnabled(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
+        return bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(filePreferences.shouldAutoRenameFilesOnChange());
+    }
+
     @Subscribe
     public void listen(FieldChangedEvent event) {
-        if (!bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(filePreferences.shouldAutoRenameFilesOnChange())
+        if (!isEnabled(bibDatabaseContext, filePreferences)
                 || filePreferences.getFileNamePattern().isEmpty()
                 || filePreferences.getFileNamePattern() == null) {
             return;
diff --git a/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java b/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
index 7165b2e50604..c7c6869aa976 100644
--- a/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
+++ b/jabgui/src/main/java/org/jabref/gui/importer/actions/OpenDirectoryLibraryAction.java
@@ -19,6 +19,7 @@
 import org.jabref.gui.clipboard.ClipBoardManager;
 import org.jabref.gui.desktop.os.NativeDesktop;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+import org.jabref.gui.externalfiles.AutoRenameFileOnEntryChange;
 import org.jabref.gui.git.GitConflictResolverDialog;
 import org.jabref.gui.git.GuiGitConflictResolverStrategy;
 import org.jabref.gui.preferences.GuiPreferences;
@@ -163,7 +164,7 @@ private void showLibraryTab(DirectoryLibraryScanner.ScanResult scanResult, PdfEn
         // Evaluated per write, so a changed preference (global or library) takes effect immediately
         // [impl->req~directory-library.pattern-rename~2]
         Function<BibEntry, Optional<String>> fileNameGenerator = entry ->
-                databaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(preferences.getFilePreferences().shouldAutoRenameFilesOnChange())
+                AutoRenameFileOnEntryChange.isEnabled(databaseContext, preferences.getFilePreferences())
                 ? FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileNamePattern())
                 : Optional.empty();
         GuiGitConflictResolverStrategy conflictResolver = new GuiGitConflictResolverStrategy(
diff --git a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
index 8ddd7c00086d..ac385bcf74e2 100644
--- a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
+++ b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
@@ -34,6 +34,7 @@
 
 class AutoRenameFileOnEntryChangeTest {
     private FilePreferences filePreferences;
+    private BibDatabaseContext bibDatabaseContext;
     private BibEntry entry;
     private Path tempDir;
 
@@ -42,7 +43,7 @@ void setUp(@TempDir Path tempDir) {
         this.tempDir = tempDir;
         MetaData metaData = new MetaData();
         metaData.setLibrarySpecificFileDirectory(tempDir.toString());
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
+        bibDatabaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
         GlobalCitationKeyPatterns keyPattern = GlobalCitationKeyPatterns.fromPattern("[auth][year]");
         GuiPreferences guiPreferences = mock(GuiPreferences.class);
         filePreferences = mock(FilePreferences.class);
@@ -110,6 +111,32 @@ void noFileRenameOnEmptyFilePattern() throws IOException {
         assertFileExists(tempDir.resolve("oldKey2081.pdf"));
     }
 
+    @Test
+    void libraryOverrideEnablesRenameDespiteDisabledGlobalPreference() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(false);
+        bibDatabaseContext.getMetaData().setAutoRenameFilesOnChange(true);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("newKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("newKey2081.pdf"));
+    }
+
+    @Test
+    void libraryOverrideDisablesRenameDespiteEnabledGlobalPreference() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(true);
+        bibDatabaseContext.getMetaData().setAutoRenameFilesOnChange(false);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("oldKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("oldKey2081.pdf"));
+    }
+
     @Test
     void singleFileRenameOnEntryChange() throws IOException {
         Files.createFile(tempDir.resolve("oldKey2081.pdf"));
diff --git a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
index ea9be3d99965..29efca1f3597 100644
--- a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
+++ b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
@@ -162,7 +162,13 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (MetaData.GIT_AUTO_PUSH.equals(entry.getKey())) {
                 metaData.setGitAutoPush(Boolean.parseBoolean(getSingleItem(values)));
             } else if (MetaData.AUTO_RENAME_FILES_ON_CHANGE.equals(entry.getKey())) {
-                metaData.setAutoRenameFilesOnChange(Boolean.parseBoolean(getSingleItem(values)));
+                // Only explicit values override the global preference; anything else leaves it in effect
+                String value = getSingleItem(values);
+                if ("true".equalsIgnoreCase(value) || "false".equalsIgnoreCase(value)) {
+                    metaData.setAutoRenameFilesOnChange(Boolean.parseBoolean(value));
+                } else {
+                    LOGGER.warn("Ignoring invalid value '{}' for {}", value, MetaData.AUTO_RENAME_FILES_ON_CHANGE);
+                }
             } else if (MetaData.SAVE_ORDER_CONFIG.equals(entry.getKey())) {
                 metaData.setSaveOrder(SaveOrder.parse(values));
             } else if (MetaData.GROUPSTREE.equals(entry.getKey()) || MetaData.GROUPSTREE_LEGACY.equals(entry.getKey())) {
diff --git a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
index bd5eb0116653..5aef6e69acfb 100644
--- a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
+++ b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
@@ -1024,7 +1024,7 @@ void userGroupsFromMirrorMetadataAreRestoredAtOpen() throws IOException, Interru
                 children.stream().map(child -> child.getGroup().getClass()).toList());
         assertEquals("My group", children.getLast().getName());
         // Membership lives in the entry's groups field and must survive the sidecar round trip
-        assertTrue(children.getLast().getGroup().contains(entries().getFirst()));
+        assertEquals(Optional.of("My group"), entries().getFirst().getField(StandardField.GROUPS));
     }
 
     /// [utest->req~directory-library.convert~1]
diff --git a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
index e180562e5d82..4c82e7b9b447 100644
--- a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
+++ b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
@@ -252,8 +252,8 @@ void mergeWritesGroupMembershipAndReadsItBack() {
                     type: article
                     title: Some Title
                 """);
-        BibEntry entry = HayagrivaMapping.toBibEntry("key", node);
-        entry.setField(StandardField.GROUPS, "Reading list, Favorites");
+        BibEntry entry = HayagrivaMapping.toBibEntry("key", node)
+                .withField(StandardField.GROUPS, "Reading list, Favorites");
 
         writer.mergeIntoNode(entry, node);
 
diff --git a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
index 6b15204ca446..0545038bc4f3 100644
--- a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
+++ b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
@@ -114,6 +114,14 @@ void parsesAutoRenameFilesOnChangeOverride() throws ParseException {
         assertEquals(Optional.of(false), parsed.getAutoRenameFilesOnChange());
     }
 
+    @Test
+    void ignoresMalformedAutoRenameFilesOnChangeOverride() throws ParseException {
+        MetaDataParser parser = new MetaDataParser(new DummyFileUpdateMonitor());
+        MetaData parsed = parser.parse(Map.of(MetaData.AUTO_RENAME_FILES_ON_CHANGE, "yes;"), ',', "userAndHost");
+
+        assertEquals(Optional.empty(), parsed.getAutoRenameFilesOnChange());
+    }
+
     @Test
     void parsesKeywordSeparator() throws ParseException {
         MetaDataParser parser = new MetaDataParser(new DummyFileUpdateMonitor());

From b423caee451b552e3d242df57acbdd3075553b62 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:15:26 +0200
Subject: [PATCH 05/13] Apply CI formatting patch

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../org/jabref/logic/exporter/HayagrivaEntryWriterTest.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
index 4c82e7b9b447..911b7428df11 100644
--- a/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
+++ b/jablib/src/test/java/org/jabref/logic/exporter/HayagrivaEntryWriterTest.java
@@ -253,7 +253,7 @@ void mergeWritesGroupMembershipAndReadsItBack() {
                     title: Some Title
                 """);
         BibEntry entry = HayagrivaMapping.toBibEntry("key", node)
-                .withField(StandardField.GROUPS, "Reading list, Favorites");
+                                         .withField(StandardField.GROUPS, "Reading list, Favorites");
 
         writer.mergeIntoNode(entry, node);
 

From e11f3bfdce0c87abde7fffbdcd1a12a7a7f19fe9 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:18:42 +0200
Subject: [PATCH 06/13] Read the global rename preference lazily, group the new
 l10n keys

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../gui/externalfiles/AutoRenameFileOnEntryChange.java      | 2 +-
 jablib/src/main/resources/l10n/JabRef_en.properties         | 6 +++---
 .../directorylibrary/DirectoryLibrarySynchronizerTest.java  | 1 -
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
index d414f7ab7d46..b9226d76bd3d 100644
--- a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
+++ b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
@@ -26,7 +26,7 @@ public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePr
 
     /// The library properties override the global preference when set (`MetaData#getAutoRenameFilesOnChange`).
     public static boolean isEnabled(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
-        return bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElse(filePreferences.shouldAutoRenameFilesOnChange());
+        return bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElseGet(filePreferences::shouldAutoRenameFilesOnChange);
     }
 
     @Subscribe
diff --git a/jablib/src/main/resources/l10n/JabRef_en.properties b/jablib/src/main/resources/l10n/JabRef_en.properties
index 75cdf0d6b46b..14dcbe4dbb1d 100644
--- a/jablib/src/main/resources/l10n/JabRef_en.properties
+++ b/jablib/src/main/resources/l10n/JabRef_en.properties
@@ -1144,6 +1144,9 @@ Use\ custom\ file\ browser=Use custom file browser
 Use\ custom\ terminal\ emulator=Use custom terminal emulator
 Linked\ file\ name\ conventions=Linked file name conventions
 Auto\ rename\ files\ if\ entry\ changes=Auto rename files if entry changes
+Use\ global\ preference\ (%0)=Use global preference (%0)
+Yes=Yes
+No=No
 Filename\ format\ pattern=Filename format pattern
 Filename\ format\ pattern\ (from\ preferences)=Filename format pattern (from preferences)
 Additional\ parameters=Additional parameters
@@ -3741,6 +3744,3 @@ Move\ group=Move group
 Sort\ subgroups=Sort subgroups
 Change\ string\ constants=Change string constants
 Founded\ by\ Morten\ O.\ Alver\ and\ Nizar\ Batada.=Founded by Morten O. Alver and Nizar Batada.
-Use\ global\ preference\ (%0)=Use global preference (%0)
-Yes=Yes
-No=No
diff --git a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
index 5aef6e69acfb..d237572ce896 100644
--- a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
+++ b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
@@ -1023,7 +1023,6 @@ void userGroupsFromMirrorMetadataAreRestoredAtOpen() throws IOException, Interru
         assertEquals(List.of(DirectoryStructureGroup.class, ExplicitGroup.class),
                 children.stream().map(child -> child.getGroup().getClass()).toList());
         assertEquals("My group", children.getLast().getName());
-        // Membership lives in the entry's groups field and must survive the sidecar round trip
         assertEquals(Optional.of("My group"), entries().getFirst().getField(StandardField.GROUPS));
     }
 

From 1f4c55209ffc39b6e8f603ba95fa77c5e3fa0ce3 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:22:46 +0200
Subject: [PATCH 07/13] Report the rename override in the metadata diff

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../metedatachange/MetadataChangeDetailsView.java   |  2 ++
 .../logic/bibtex/comparator/MetaDataDiff.java       |  2 ++
 .../logic/bibtex/comparator/MetaDataDiffTest.java   | 13 +++++++++++++
 3 files changed, 17 insertions(+)

diff --git a/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java b/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
index 696e8cfa738d..f3a5c732b2e2 100644
--- a/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
+++ b/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
@@ -106,6 +106,8 @@ private String getDifferenceString(MetaDataDiff.DifferenceType changeType) {
                     Localization.lang("Library-specific file directory");
             case CONTENT_SELECTOR ->
                     Localization.lang("Content selectors");
+            case AUTO_RENAME_FILES_ON_CHANGE ->
+                    Localization.lang("Auto rename files if entry changes");
         };
     }
 }
diff --git a/jablib/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java b/jablib/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java
index 2c8c835dec12..d2687571dc89 100644
--- a/jablib/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java
+++ b/jablib/src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java
@@ -16,6 +16,7 @@
 
 public class MetaDataDiff {
     public enum DifferenceType {
+        AUTO_RENAME_FILES_ON_CHANGE,
         CONTENT_SELECTOR,
         DEFAULT_KEY_PATTERN,
         ENCODING,
@@ -112,6 +113,7 @@ public List<Difference> getDifferences(GlobalCitationKeyPatterns globalCitationK
         addToListIfDiff(changes, DifferenceType.MODE, originalMetaData.getMode(), newMetaData.getMode());
         addToListIfDiff(changes, DifferenceType.LIBRARY_SPECIFIC_FILE_DIRECTORY, originalMetaData.getLibrarySpecificFileDirectory(), newMetaData.getLibrarySpecificFileDirectory());
         addToListIfDiff(changes, DifferenceType.CONTENT_SELECTOR, originalMetaData.getContentSelectors(), newMetaData.getContentSelectors());
+        addToListIfDiff(changes, DifferenceType.AUTO_RENAME_FILES_ON_CHANGE, originalMetaData.getAutoRenameFilesOnChange(), newMetaData.getAutoRenameFilesOnChange());
         return changes;
     }
 
diff --git a/jablib/src/test/java/org/jabref/logic/bibtex/comparator/MetaDataDiffTest.java b/jablib/src/test/java/org/jabref/logic/bibtex/comparator/MetaDataDiffTest.java
index 542e816786bb..222910385f06 100644
--- a/jablib/src/test/java/org/jabref/logic/bibtex/comparator/MetaDataDiffTest.java
+++ b/jablib/src/test/java/org/jabref/logic/bibtex/comparator/MetaDataDiffTest.java
@@ -3,6 +3,7 @@
 import java.util.List;
 import java.util.Optional;
 
+import org.jabref.logic.citationkeypattern.GlobalCitationKeyPatterns;
 import org.jabref.logic.groups.GroupsFactory;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.groups.ExplicitGroup;
@@ -18,6 +19,7 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.mockito.Mockito.mock;
 
 @ResourceLock("Localization.lang")
 @Execution(ExecutionMode.SAME_THREAD)
@@ -32,6 +34,17 @@ void compareWithSameContentSelectorsDoesNotReportAnyDiffs() {
         assertEquals(Optional.empty(), MetaDataDiff.compare(one, two));
     }
 
+    @Test
+    void autoRenameOverrideIsReported() {
+        MetaData one = new MetaData();
+        MetaData two = new MetaData();
+        two.setAutoRenameFilesOnChange(false);
+
+        List<MetaDataDiff.Difference> differences = MetaDataDiff.compare(one, two).orElseThrow().getDifferences(mock(GlobalCitationKeyPatterns.class));
+
+        assertEquals(List.of(new MetaDataDiff.Difference(MetaDataDiff.DifferenceType.AUTO_RENAME_FILES_ON_CHANGE, Optional.empty(), Optional.of(false))), differences);
+    }
+
     @Test
     void defaultSettingEqualsEmptySetting() {
         MetaData one = new MetaData();

From 176c3dbbf87ef58c8a131ac3cd3c43112577f42d Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:28:53 +0200
Subject: [PATCH 08/13] Skip renames without a filename pattern, label the
 override in the change dialog

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../metedatachange/MetadataChangeDetailsView.java | 15 +++++++++++++--
 .../AutoRenameFileOnEntryChange.java              | 11 ++++++-----
 .../src/main/resources/l10n/JabRef_en.properties  |  1 +
 3 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java b/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
index f3a5c732b2e2..112e30ed7715 100644
--- a/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
+++ b/jabgui/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
@@ -1,5 +1,7 @@
 package org.jabref.gui.collab.metedatachange;
 
+import java.util.Optional;
+
 import javafx.scene.control.Label;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.layout.VBox;
@@ -72,14 +74,23 @@ private ScrollPane createDefaultDiffScrollPane(MetaDataDiff.Difference diff) {
         VBox diffContainer = new VBox(12);
 
         // Show both original and new values
-        diffContainer.getChildren().add(new Label(diff.originalObject().toString()));
-        diffContainer.getChildren().add(new Label(diff.newObject().toString()));
+        diffContainer.getChildren().add(new Label(formatValue(diff, diff.originalObject())));
+        diffContainer.getChildren().add(new Label(formatValue(diff, diff.newObject())));
 
         ScrollPane scrollPane = new ScrollPane(diffContainer);
         scrollPane.setFitToWidth(true);
         return scrollPane;
     }
 
+    private static String formatValue(MetaDataDiff.Difference diff, Object value) {
+        if (diff.differenceType() == MetaDataDiff.DifferenceType.AUTO_RENAME_FILES_ON_CHANGE
+                && value instanceof Optional<?> override) {
+            return override.map(rename -> Boolean.TRUE.equals(rename) ? Localization.lang("Yes") : Localization.lang("No"))
+                           .orElse(Localization.lang("Use global preference"));
+        }
+        return value.toString();
+    }
+
     private String getDifferenceString(MetaDataDiff.DifferenceType changeType) {
         return switch (changeType) {
             case PROTECTED ->
diff --git a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
index b9226d76bd3d..e6307686211c 100644
--- a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
+++ b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
@@ -2,6 +2,7 @@
 
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.cleanup.RenamePdfCleanup;
+import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.FieldChangedEvent;
@@ -24,16 +25,16 @@ public AutoRenameFileOnEntryChange(BibDatabaseContext bibDatabaseContext, FilePr
         renamePdfCleanup = new RenamePdfCleanup(false, () -> bibDatabaseContext, filePreferences);
     }
 
-    /// The library properties override the global preference when set (`MetaData#getAutoRenameFilesOnChange`).
+    /// The library properties override the global preference when set (`MetaData#getAutoRenameFilesOnChange`);
+    /// without a filename pattern there is nothing to rename to.
     public static boolean isEnabled(BibDatabaseContext bibDatabaseContext, FilePreferences filePreferences) {
-        return bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElseGet(filePreferences::shouldAutoRenameFilesOnChange);
+        return !StringUtil.isBlank(filePreferences.getFileNamePattern())
+                && bibDatabaseContext.getMetaData().getAutoRenameFilesOnChange().orElseGet(filePreferences::shouldAutoRenameFilesOnChange);
     }
 
     @Subscribe
     public void listen(FieldChangedEvent event) {
-        if (!isEnabled(bibDatabaseContext, filePreferences)
-                || filePreferences.getFileNamePattern().isEmpty()
-                || filePreferences.getFileNamePattern() == null) {
+        if (!isEnabled(bibDatabaseContext, filePreferences)) {
             return;
         }
 
diff --git a/jablib/src/main/resources/l10n/JabRef_en.properties b/jablib/src/main/resources/l10n/JabRef_en.properties
index 14dcbe4dbb1d..7dab966dd984 100644
--- a/jablib/src/main/resources/l10n/JabRef_en.properties
+++ b/jablib/src/main/resources/l10n/JabRef_en.properties
@@ -1144,6 +1144,7 @@ Use\ custom\ file\ browser=Use custom file browser
 Use\ custom\ terminal\ emulator=Use custom terminal emulator
 Linked\ file\ name\ conventions=Linked file name conventions
 Auto\ rename\ files\ if\ entry\ changes=Auto rename files if entry changes
+Use\ global\ preference=Use global preference
 Use\ global\ preference\ (%0)=Use global preference (%0)
 Yes=Yes
 No=No

From 73ef5ad23b8b9722e5c69a03bb31f03ed46f0a45 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:33:37 +0200
Subject: [PATCH 09/13] Leave folder-library renames to the sidecar write-back

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../externalfiles/AutoRenameFileOnEntryChange.java  |  4 +++-
 .../AutoRenameFileOnEntryChangeTest.java            | 13 +++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
index e6307686211c..a32f3f52c874 100644
--- a/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
+++ b/jabgui/src/main/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChange.java
@@ -2,6 +2,7 @@
 
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.cleanup.RenamePdfCleanup;
+import org.jabref.logic.shared.DatabaseLocation;
 import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -34,7 +35,8 @@ public static boolean isEnabled(BibDatabaseContext bibDatabaseContext, FilePrefe
 
     @Subscribe
     public void listen(FieldChangedEvent event) {
-        if (!isEnabled(bibDatabaseContext, filePreferences)) {
+        // A directory library renames its sidecar/PDF pairs in the write-back (see SidecarWriteBack)
+        if (bibDatabaseContext.getLocation() == DatabaseLocation.DIRECTORY || !isEnabled(bibDatabaseContext, filePreferences)) {
             return;
         }
 
diff --git a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
index ac385bcf74e2..ca0011ff12f9 100644
--- a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
+++ b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoRenameFileOnEntryChangeTest.java
@@ -137,6 +137,19 @@ void libraryOverrideDisablesRenameDespiteEnabledGlobalPreference() throws IOExce
         assertFileExists(tempDir.resolve("oldKey2081.pdf"));
     }
 
+    @Test
+    void directoryLibrariesLeaveRenamesToTheSidecarWriteBack() throws IOException {
+        Files.createFile(tempDir.resolve("oldKey2081.pdf"));
+        entry.setFiles(List.of(new LinkedFile("", "oldKey2081.pdf", "PDF")));
+        when(filePreferences.shouldAutoRenameFilesOnChange()).thenReturn(true);
+        bibDatabaseContext.convertToDirectoryLibrary(tempDir);
+
+        entry.setField(StandardField.AUTHOR, "newKey");
+
+        assertEquals("oldKey2081.pdf", entry.getFiles().getFirst().getLink());
+        assertFileExists(tempDir.resolve("oldKey2081.pdf"));
+    }
+
     @Test
     void singleFileRenameOnEntryChange() throws IOException {
         Files.createFile(tempDir.resolve("oldKey2081.pdf"));

From 7e49b4216bb3c62092733b8dce2f5c74bbf2e74b Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:37:06 +0200
Subject: [PATCH 10/13] Clear a stale rename override on a malformed value

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../java/org/jabref/logic/importer/util/MetaDataParser.java | 1 +
 .../org/jabref/logic/importer/util/MetaDataParserTest.java  | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
index 29efca1f3597..c3f2752c2ec7 100644
--- a/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
+++ b/jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
@@ -168,6 +168,7 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
                     metaData.setAutoRenameFilesOnChange(Boolean.parseBoolean(value));
                 } else {
                     LOGGER.warn("Ignoring invalid value '{}' for {}", value, MetaData.AUTO_RENAME_FILES_ON_CHANGE);
+                    metaData.clearAutoRenameFilesOnChange();
                 }
             } else if (MetaData.SAVE_ORDER_CONFIG.equals(entry.getKey())) {
                 metaData.setSaveOrder(SaveOrder.parse(values));
diff --git a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
index 0545038bc4f3..481cd791a7e6 100644
--- a/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
+++ b/jablib/src/test/java/org/jabref/logic/importer/util/MetaDataParserTest.java
@@ -115,9 +115,11 @@ void parsesAutoRenameFilesOnChangeOverride() throws ParseException {
     }
 
     @Test
-    void ignoresMalformedAutoRenameFilesOnChangeOverride() throws ParseException {
+    void malformedAutoRenameFilesOnChangeOverrideClearsThePreviousOne() throws ParseException {
+        MetaData existing = new MetaData();
+        existing.setAutoRenameFilesOnChange(true);
         MetaDataParser parser = new MetaDataParser(new DummyFileUpdateMonitor());
-        MetaData parsed = parser.parse(Map.of(MetaData.AUTO_RENAME_FILES_ON_CHANGE, "yes;"), ',', "userAndHost");
+        MetaData parsed = parser.parse(existing, Map.of(MetaData.AUTO_RENAME_FILES_ON_CHANGE, "yes;"), ',', "userAndHost");
 
         assertEquals(Optional.empty(), parsed.getAutoRenameFilesOnChange());
     }

From 7b2b3d722bc16d50b4d6fddf53f59936fceab1c4 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 14 Sep 2026 00:43:59 +0200
Subject: [PATCH 11/13] Populate the rename override in the metadata copy
 fixture

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7bhV1r2H2XZvjHrYQkiJt
---
 .../org/jabref/model/metadata/MetaDataOverwriteWithTest.java     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/jablib/src/test/java/org/jabref/model/metadata/MetaDataOverwriteWithTest.java b/jablib/src/test/java/org/jabref/model/metadata/MetaDataOverwriteWithTest.java
index 42124b7b9d4e..c9028a44963c 100644
--- a/jablib/src/test/java/org/jabref/model/metadata/MetaDataOverwriteWithTest.java
+++ b/jablib/src/test/java/org/jabref/model/metadata/MetaDataOverwriteWithTest.java
@@ -80,6 +80,7 @@ private static MetaData populated() {
         metaData.setGitAutoPull(true);
         metaData.setGitAutoCommit(true);
         metaData.setGitAutoPush(true);
+        metaData.setAutoRenameFilesOnChange(true);
         metaData.setCiteKeyPattern(new CitationKeyPattern("[auth]", CitationKeyPattern.Category.AUTHOR_RELATED),
                 Map.of(StandardEntryType.Article, new CitationKeyPattern("[auth][year]", CitationKeyPattern.Category.AUTHOR_RELATED)));
         metaData.setSaveActions(new FieldFormatterCleanupActions(true, List.of()));

From 5ece0541be137feb60607363a2006499a38f870b Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Wed, 23 Sep 2026 15:10:52 +0200
Subject: [PATCH 12/13] Move #769 CHANGELOG entry to Unreleased

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7b3acfa42163..759a6d819756 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#769](https://github.com/JabRef/jabref-koppor/pull/769)
 - In directory libraries, a sidecar and its PDF are now renamed together to the configured filename pattern (Preferences > Linked files) whenever the entry is edited — e.g. changing the citation key renames both files. [#741](https://github.com/JabRef/jabref-koppor/pull/741)
 - The groups panel of a directory library now mirrors the folder structure: each subdirectory appears as a group containing the entries whose files live there (updated live as files change). [#740](https://github.com/JabRef/jabref-koppor/pull/740)
 - Directory libraries now save into their sidecar files: edits are written back automatically (debounced until typing pauses; Ctrl+S forces the write and no longer creates a `.bib`), the first edit of a PDF-only entry creates a Markdown sidecar (`X.md` with the Hayagriva data as frontmatter and the comment fields as notes body), renaming a citation key renames the YAML key, and deleting an entry removes it from its file (the file is trashed once empty, the PDF stays). Hand-written content that JabRef does not understand survives rewrites. [#739](https://github.com/JabRef/jabref-koppor/pull/739)
@@ -108,7 +109,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added OCR language selection to the OCR preferences, allowing users to configure which Tesseract languages to use. [#16618](https://github.com/JabRef/jabref/issues/16618)
 - We added a fetcher for the Bielefeld Academic Search Engine (BASE). [#15016](https://github.com/JabRef/jabref/issues/15016)
 - We added a Git section to the library properties for automatic commit, pull and push. [#12630](https://github.com/JabRef/jabref/issues/12630)
-- We added a library-specific override of the "Auto rename files if entry changes" preference to the library properties. [#769](https://github.com/JabRef/jabref-koppor/pull/769)
 - We added connection URL pasting to the shared database login dialog. [#16800](https://github.com/JabRef/jabref/pull/16800)
 - We added a Dnb Fetcher that uses SRU interface and wired to ISBN Fetcher. [#17070](https://github.com/JabRef/jabref/pull/17070)
 - We added read-only access to shared SQL libraries in `jabkit`: every input file argument accepts a PostgreSQL URL. [#12948](https://github.com/JabRef/jabref/issues/12948)

From c5f12b8760f04286394b1eeb8cdd590eb4c823f1 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Wed, 23 Sep 2026 15:12:57 +0200
Subject: [PATCH 13/13] Restore keyword separator and rename override of folder
 libraries on reopen

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .../logic/directorylibrary/BibMirror.java     | 26 ++++++++++++++++---
 .../DirectoryLibrarySynchronizerTest.java     | 25 ++++++++++++++++++
 2 files changed, 48 insertions(+), 3 deletions(-)

diff --git a/jablib/src/main/java/org/jabref/logic/directorylibrary/BibMirror.java b/jablib/src/main/java/org/jabref/logic/directorylibrary/BibMirror.java
index b794931748f4..6fdbf3d48819 100644
--- a/jablib/src/main/java/org/jabref/logic/directorylibrary/BibMirror.java
+++ b/jablib/src/main/java/org/jabref/logic/directorylibrary/BibMirror.java
@@ -20,6 +20,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.groups.DirectoryStructureGroup;
 import org.jabref.model.groups.GroupTreeNode;
+import org.jabref.model.metadata.MetaData;
 
 import org.jspecify.annotations.NullMarked;
 import org.slf4j.Logger;
@@ -120,9 +121,12 @@ void doInitialize() {
                 writeScheduler.accept(mirror);
                 return;
             }
-            // The mirror's metadata is the only place user-defined groups of a directory
-            // library survive a restart — the sidecars carry entries, not library metadata
-            readBibContext(mirror).ifPresent(this::adoptUserGroups);
+            // The mirror's metadata is the only place library settings and user-defined groups of
+            // a directory library survive a restart — the sidecars carry entries, not library metadata
+            readBibContext(mirror).ifPresent(remote -> {
+                adoptLibrarySettings(remote);
+                adoptUserGroups(remote);
+            });
             try {
                 if (Files.exists(baseFile(root)) && Files.mismatch(mirror, baseFile(root)) == -1L) {
                     return;
@@ -180,6 +184,22 @@ private void merge(BibDatabaseContext remote) {
         markDirty();
     }
 
+    /// Restores the library properties that the sidecars do not carry. The keyword separator
+    /// comes first: explicit group memberships in the sidecars are separated by it.
+    private void adoptLibrarySettings(BibDatabaseContext remote) {
+        MetaData remoteMetaData = remote.getMetaData();
+        Optional<Character> keywordSeparator = remoteMetaData.getKeywordSeparator();
+        Optional<Boolean> autoRename = remoteMetaData.getAutoRenameFilesOnChange();
+        if (keywordSeparator.isEmpty() && autoRename.isEmpty()) {
+            return;
+        }
+        modelUpdateMarshaller.accept(() -> {
+            MetaData metaData = databaseContext.getMetaData();
+            keywordSeparator.ifPresent(metaData::setKeywordSeparator);
+            autoRename.ifPresent(metaData::setAutoRenameFilesOnChange);
+        });
+    }
+
     /// Restores user-defined groups from the mirror's metadata into the freshly scanned
     /// context (whose tree only holds the automatic directory-structure group). The
     /// serialized directory-structure group itself is skipped — the scanner installs it with
diff --git a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
index d237572ce896..5759863f288c 100644
--- a/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
+++ b/jablib/src/test/java/org/jabref/logic/directorylibrary/DirectoryLibrarySynchronizerTest.java
@@ -51,6 +51,8 @@
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.groups.event.GroupUpdatedEvent;
 import org.jabref.model.metadata.SaveOrder;
+import org.jabref.model.metadata.event.MetaDataChangeSource;
+import org.jabref.model.metadata.event.MetaDataChangedEvent;
 
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
@@ -1026,6 +1028,29 @@ void userGroupsFromMirrorMetadataAreRestoredAtOpen() throws IOException, Interru
         assertEquals(Optional.of("My group"), entries().getFirst().getField(StandardField.GROUPS));
     }
 
+    /// [utest->req~directory-library.bib-mirror~2]
+    @Test
+    void librarySettingsFromMirrorMetadataAreRestoredAtOpen() throws IOException, InterruptedException, ExecutionException {
+        Files.writeString(root.resolve("smith2020.yml"), ARTICLE_YAML);
+        openLibrary();
+        synchronizer.doInitializeMirror();
+        synchronizer.flush();
+        context.getMetaData().setKeywordSeparator(';');
+        context.getMetaData().setAutoRenameFilesOnChange(false);
+        // Delivered by the context's change filter in the application
+        synchronizer.listen(new MetaDataChangedEvent(context.getMetaData(), MetaDataChangeSource.LOCAL));
+        synchronizer.awaitPendingEvents();
+        synchronizer.flush();
+        synchronizer.shutdown();
+
+        openLibrary();
+        synchronizer.doInitializeMirror();
+        synchronizer.flush();
+
+        assertEquals(Optional.of(';'), context.getMetaData().getKeywordSeparator());
+        assertEquals(Optional.of(false), context.getMetaData().getAutoRenameFilesOnChange());
+    }
+
     /// [utest->req~directory-library.convert~1]
     @Test
     void convertedLibraryReopensWithoutMerge() throws IOException, InterruptedException, ExecutionException {