Implement logic orchestration for Git Pull/Push operations

docs/code-howtos/git.md

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+# git
+
+## Conflict Scenarios
+
+- **T1.** Remote changed a field, local did not  
+  → No conflict.  
+  The local version remained unchanged, so the remote change can be safely applied.
+
+- **T2.** Local changed a field, remote did not  
+  → No conflict.  
+  The remote version did not touch the field, so the local change is preserved.
+
+- **T3.** Both local and remote changed the same field to the same value  
+  → No conflict.  
+  Although both sides changed the field, the result is identical—therefore, no conflict.
+
+- **T4.** Both local and remote changed the same field to different values  
+  → Conflict.  
+  This is a true semantic conflict that requires resolution.
+
+- **T5.** Local deleted a field, remote modified the same field  
+  → Conflict.  
+  One side deleted the field while the other updated it—this is contradictory.
+
+- **T6.** Local modified a field, remote deleted it  
+  → Conflict.  
+  Similar to T5, one side deletes, the other edits—this is a conflict.
+
+- **T7.** Local unchanged, remote deleted a field  
+  → No conflict.  
+  Local did not modify anything, so remote deletion is accepted.
+
+- **T8.** Local changed field A, remote changed field B (within the same entry)  
+  → No conflict.  
+  Changes are on separate fields, so they can be merged safely.
+
+- **T9.** Both changed the same entry, but only field order changed  
+  → No conflict.  
+  Field order is not semantically meaningful, so no conflict is detected.
+
+- **T10.** Local modified entry A, remote modified entry B  
+  → No conflict.  
+  Modifications are on different entries, which are always safe to merge.
+
+- **T11.** Remote added a new field, local did nothing  
+  → No conflict.  
+  Remote addition can be applied without issues.
+
+- **T12.** Remote added a field, local also added the same field, but with different value  
+  → Conflict.  
+  One side added while the other side modified—there is a semantic conflict.
+
+- **T13.** Local added a field, remote did nothing  
+  → No conflict.  
+  Safe to preserve the local addition.
+
+- **T14.** Both added the same field with the same value  
+  → No conflict.  
+  Even though both sides added it, the value is the same—no need for resolution.
+
+- **T15.** Both added the same field with different values  
+  → Conflict.  
+  The same field is introduced with different values, which creates a conflict.
+
+- **T16.** Both added the same entry key with different values  
+  → Conflict.  
+  Both sides created a new entry with the same citation key, but the fields differ.
+
+- **T17.** Both added the same entry key with identical values  
+  → No conflict.  
+  Both sides created a new entry with the same citation key and identical fields, so it can be merged safely.

jabgui/src/main/java/org/jabref/gui/git/GitConflictResolverDialog.java

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+package org.jabref.gui.git;
+
+import java.util.Optional;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.mergeentries.MergeEntriesDialog;
+import org.jabref.gui.mergeentries.newmergedialog.ShowDiffConfig;
+import org.jabref.gui.mergeentries.newmergedialog.diffhighlighter.DiffHighlighter;
+import org.jabref.gui.mergeentries.newmergedialog.toolbar.ThreeWayMergeToolbar;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.logic.git.conflicts.ThreeWayEntryConflict;
+import org.jabref.model.entry.BibEntry;
+
+/**
+ * UI wrapper
+ * Receives a semantic conflict (ThreeWayEntryConflict), pops up an interactive GUI (belonging to mergeentries), and returns a user-confirmed BibEntry merge result.
+ */
+public class GitConflictResolverDialog {
+    private final DialogService dialogService;
+    private final GuiPreferences preferences;
+
+    public GitConflictResolverDialog(DialogService dialogService, GuiPreferences preferences) {
+        this.dialogService = dialogService;
+        this.preferences = preferences;
+    }
+
+    public Optional<BibEntry> resolveConflict(ThreeWayEntryConflict conflict) {
+        BibEntry base = conflict.base();
+        BibEntry local = conflict.local();
+        BibEntry remote = conflict.remote();
+
+        // Create Dialog + Set Title + Configure Diff Highlighting
+        MergeEntriesDialog dialog = new MergeEntriesDialog(local, remote, preferences);
+        dialog.setLeftHeaderText("Local");
+        dialog.setRightHeaderText("Remote");
+        ShowDiffConfig diffConfig = new ShowDiffConfig(
+                ThreeWayMergeToolbar.DiffView.SPLIT,
+                DiffHighlighter.BasicDiffMethod.WORDS
+        );
+        dialog.configureDiff(diffConfig);
+
+        return dialogService.showCustomDialogAndWait(dialog)
+                            .map(result -> result.mergedEntry());
+    }
+}

jabgui/src/main/java/org/jabref/gui/git/GitPullAction.java

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+package org.jabref.gui.git;
+
+import java.io.IOException;
+import java.nio.file.Path;
+
+import javax.swing.undo.UndoManager;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.logic.JabRefException;
+import org.jabref.logic.git.GitHandler;
+import org.jabref.logic.git.GitSyncService;
+import org.jabref.logic.git.conflicts.GitConflictResolverStrategy;
+import org.jabref.logic.git.model.MergeResult;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.eclipse.jgit.api.errors.GitAPIException;
+
+/**
+ * - Check if Git is enabled
+ * - Verify activeDatabase is not null
+ * - Call GitPullViewModel.pull()
+ */
+public class GitPullAction extends SimpleCommand {
+
+    private final DialogService dialogService;
+    private final StateManager stateManager;
+    private final GuiPreferences guiPreferences;
+    private final UndoManager undoManager;
+
+    public GitPullAction(DialogService dialogService,
+                         StateManager stateManager,
+                         GuiPreferences guiPreferences,
+                         UndoManager undoManager) {
+        this.dialogService = dialogService;
+        this.stateManager = stateManager;
+        this.guiPreferences = guiPreferences;
+        this.undoManager = undoManager;
+    }
+
+    @Override
+    public void execute() {
+        // TODO: reconsider error handling
+        if (stateManager.getActiveDatabase().isEmpty()) {
+            dialogService.showErrorDialogAndWait("No database open", "Please open a database before pulling.");
+            return;
+        }
+
+        BibDatabaseContext database = stateManager.getActiveDatabase().get();
+        if (database.getDatabasePath().isEmpty()) {
+            dialogService.showErrorDialogAndWait("No .bib file path", "Cannot pull from Git: No file is associated with this database.");
+            return;
+        }
+
+        Path bibFilePath = database.getDatabasePath().get();
+        try {
+            GitHandler handler = new GitHandler(bibFilePath.getParent());
+            GitConflictResolverDialog dialog = new GitConflictResolverDialog(dialogService, guiPreferences);
+            GitConflictResolverStrategy resolver = new GuiConflictResolverStrategy(dialog);
+
+            GitSyncService syncService = new GitSyncService(guiPreferences.getImportFormatPreferences(), handler, resolver);
+            GitStatusViewModel statusViewModel = new GitStatusViewModel(bibFilePath);
+
+            GitPullViewModel viewModel = new GitPullViewModel(syncService, statusViewModel);
+            MergeResult result = viewModel.pull();
+
+            if (result.isSuccessful()) {
+                dialogService.showInformationDialogAndWait("Git Pull", "Successfully merged and updated.");
+            } else {
+                dialogService.showWarningDialogAndWait("Git Pull", "Merge completed with conflicts.");
+            }
+        } catch (JabRefException e) {
+            dialogService.showErrorDialogAndWait("Git Pull Failed", e);
+            // TODO: error handling
+        } catch (GitAPIException e) {
+            throw new RuntimeException(e);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

jabgui/src/main/java/org/jabref/gui/git/GitPullViewModel.java

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+package org.jabref.gui.git;
+
+import java.io.IOException;
+import java.nio.file.Path;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.logic.JabRefException;
+import org.jabref.logic.git.GitSyncService;
+import org.jabref.logic.git.model.MergeResult;
+
+import org.eclipse.jgit.api.errors.GitAPIException;
+
+public class GitPullViewModel extends AbstractViewModel {
+    private final GitSyncService syncService;
+    private final GitStatusViewModel gitStatusViewModel;
+    private final Path bibFilePath;
+
+    public GitPullViewModel(GitSyncService syncService, GitStatusViewModel gitStatusViewModel) {
+        this.syncService = syncService;
+        this.gitStatusViewModel = gitStatusViewModel;
+        this.bibFilePath = gitStatusViewModel.getCurrentBibFile();
+    }
+
+    public MergeResult pull() throws IOException, GitAPIException, JabRefException {
+        MergeResult result = syncService.fetchAndMerge(bibFilePath);
+
+        if (result.isSuccessful()) {
+            gitStatusViewModel.updateStatusFromPath(bibFilePath);
+        }
+
+        return result;
+    }
+}

jabgui/src/main/java/org/jabref/gui/git/GitStatusViewModel.java

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+package org.jabref.gui.git;
+
+import java.nio.file.Path;
+import java.util.Optional;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleObjectProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+
+import org.jabref.gui.AbstractViewModel;
+import org.jabref.logic.git.GitHandler;
+import org.jabref.logic.git.status.GitStatusChecker;
+import org.jabref.logic.git.status.GitStatusSnapshot;
+import org.jabref.logic.git.status.SyncStatus;
+
+/**
+ * ViewModel that holds current Git sync status for the open .bib database.
+ * It maintains the state of the GitHandler bound to the current file path, including:
+ * - Whether the current file is inside a Git repository
+ * - Whether the file is tracked by Git
+ * - Whether there are unresolved merge conflicts
+ * - The current sync status (e.g., UP_TO_DATE, DIVERGED, etc.)
+ */
+public class GitStatusViewModel extends AbstractViewModel {
+    private final Path currentBibFile;
+    private final ObjectProperty<SyncStatus> syncStatus = new SimpleObjectProperty<>(SyncStatus.UNTRACKED);
+    private final BooleanProperty isTracking = new SimpleBooleanProperty(false);
+    private final BooleanProperty conflictDetected = new SimpleBooleanProperty(false);
+    private final StringProperty lastPulledCommit = new SimpleStringProperty("");
+    private GitHandler activeHandler = null;
+
+    public GitStatusViewModel(Path bibFilePath) {
+        this.currentBibFile = bibFilePath;
+        updateStatusFromPath(bibFilePath);
+    }
+
+    /**
+     * Try to detect Git repository status from the given file or folder path.
+     *
+     * @param fileOrFolderInRepo Any path (file or folder) assumed to be inside a Git repository
+     */
+    public void updateStatusFromPath(Path fileOrFolderInRepo) {
+        Optional<GitHandler> maybeHandler = GitHandler.fromAnyPath(fileOrFolderInRepo);
+
+        if (maybeHandler.isEmpty()) {
+            reset();
+            return;
+        }
+
+        GitHandler handler = maybeHandler.get();
+        this.activeHandler = handler;
+
+        GitStatusSnapshot snapshot = GitStatusChecker.checkStatus(fileOrFolderInRepo);
+
+        setTracking(snapshot.tracking());
+        setSyncStatus(snapshot.syncStatus());
+        setConflictDetected(snapshot.conflict());
+        snapshot.lastPulledCommit().ifPresent(this::setLastPulledCommit);
+    }
+
+    /**
+     * Clears all internal state to defaults.
+     * Should be called when switching projects or Git context is lost
+     */
+    public void reset() {
+        setSyncStatus(SyncStatus.UNTRACKED);
+        setTracking(false);
+        setConflictDetected(false);
+        setLastPulledCommit("");
+    }
+
+    public ObjectProperty<SyncStatus> syncStatusProperty() {
+        return syncStatus;
+    }
+
+    public SyncStatus getSyncStatus() {
+        return syncStatus.get();
+    }
+
+    public void setSyncStatus(SyncStatus status) {
+        this.syncStatus.set(status);
+    }
+
+    public BooleanProperty isTrackingProperty() {
+        return isTracking;
+    }
+
+    public boolean isTracking() {
+        return isTracking.get();
+    }
+
+    public void setTracking(boolean tracking) {
+        this.isTracking.set(tracking);
+    }
+
+    public BooleanProperty conflictDetectedProperty() {
+        return conflictDetected;
+    }
+
+    public boolean isConflictDetected() {
+        return conflictDetected.get();
+    }
+
+    public void setConflictDetected(boolean conflict) {
+        this.conflictDetected.set(conflict);
+    }
+
+    public StringProperty lastPulledCommitProperty() {
+        return lastPulledCommit;
+    }
+
+    public String getLastPulledCommit() {
+        return lastPulledCommit.get();
+    }
+
+    public void setLastPulledCommit(String commitHash) {
+        this.lastPulledCommit.set(commitHash);
+    }
+
+    public Optional<GitHandler> getActiveHandler() {
+        return Optional.ofNullable(activeHandler);
+    }
+
+    public Path getCurrentBibFile() {
+        return currentBibFile;
+    }
+}

jabgui/src/main/java/org/jabref/gui/git/GuiConflictResolverStrategy.java

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+package org.jabref.gui.git;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+import org.jabref.logic.git.conflicts.GitConflictResolverStrategy;
+import org.jabref.logic.git.conflicts.ThreeWayEntryConflict;
+import org.jabref.logic.git.merge.GitMergeUtil;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+
+public class GuiConflictResolverStrategy implements GitConflictResolverStrategy {
+    private final GitConflictResolverDialog dialog;
+
+    public GuiConflictResolverStrategy(GitConflictResolverDialog dialog) {
+        this.dialog = dialog;
+    }
+
+    @Override
+    public Optional<BibDatabaseContext> resolveConflicts(List<ThreeWayEntryConflict> conflicts, BibDatabaseContext remote) {
+        List<BibEntry> resolved = new ArrayList<>();
+        for (ThreeWayEntryConflict conflict : conflicts) {
+            Optional<BibEntry> maybeConflict = dialog.resolveConflict(conflict);
+            if (maybeConflict.isEmpty()) {
+                return Optional.empty();
+            }
+            resolved.add(maybeConflict.get());
+        }
+        return Optional.of(GitMergeUtil.replaceEntries(remote, resolved));
+    }
+}