fix problems related to javadoc and indent

src/main/java/org/jabref/gui/autosaveandbackup/BackupManager.java

@@ -163,7 +163,13 @@ public static void rewriteFile(Path dbFile, String content) throws IOException {
         LOGGER.info("Successfully rewrote the file at path: {}", dbFile);
     }
 
-    // Helper method to normalize BibTeX content
+    /**
+     * Normalizes the BibTeX content by trimming spaces, removing blank lines, and reassembling with line breaks.
+     * This is needed to ensure consistent formatting of BibTeX entries, which helps in comparing and processing them.
+     *
+     * @param input The raw BibTeX content.
+     * @return The normalized BibTeX content.
+     */
     private static String normalizeBibTeX(String input) {
         if (input == null || input.isBlank()) {
             return "";
@@ -181,7 +187,15 @@ private static String normalizeBibTeX(String input) {
         return normalized;
     }
 
-    // Helper method to ensure the Git repository is initialized
+    /**
+     * Ensures that a Git repository is initialized in the specified backup directory.
+     * If the `.git` directory does not exist, it initializes a new Git repository.
+     * Then, it builds the Git object for further operations.
+     *
+     * @param backupDir The backup directory containing the Git repository.
+     * @throws IOException If an I/O error occurs.
+     * @throws GitAPIException If a Git API error occurs.
+     */
     static void ensureGitInitialized(Path backupDir) throws IOException, GitAPIException {
 
         // This method was created because the initialization of the Git object, when written in the constructor, was causing a NullPointerException
@@ -210,17 +224,22 @@ static void ensureGitInitialized(Path backupDir) throws IOException, GitAPIExcep
         git = new Git(repository);
     }
 
-    // Helper method to copy the database file to the backup directory
-    protected static void copyDatabaseFileToBackupDir(Path dbFile, Path backupDirPath) throws IOException {
+    /**
+     * Copies the database file to the backup directory with a unique file name.
+     * The unique file name is generated by appending a UUID to the original file name.
+     *
+     * @param dbFile        The path to the database file to be copied.
+     * @param backupDirPath The path to the backup directory.
+     * @throws IOException If an I/O error occurs during the file copy operation.
+     */
+        protected static void copyDatabaseFileToBackupDir(Path dbFile, Path backupDirPath) throws IOException {
         String fileUuid = getOrGenerateFileUuid(dbFile);
         String uniqueFileName = appendUuidToFileName(dbFile.getFileName().toString(), fileUuid);
         Path backupFilePath = backupDirPath.resolve(uniqueFileName);
         Files.copy(dbFile, backupFilePath, StandardCopyOption.REPLACE_EXISTING);
         LOGGER.info("Database file uniquely copied to backup directory: {}", backupFilePath);
     }
 
-    // A method
-
     /**
      * Starts a new BackupManager instance and begins the backup task.
      *
@@ -232,7 +251,6 @@ protected static void copyDatabaseFileToBackupDir(Path dbFile, Path backupDirPat
      * @throws IOException     if an I/O error occurs
      * @throws GitAPIException if a Git API error occurs
      */
-
     public static BackupManager start(LibraryTab libraryTab, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, CliPreferences preferences) throws IOException, GitAPIException {
         LOGGER.info("In methode Start");
         Path backupDir = preferences.getFilePreferences().getBackupDirectory();
@@ -265,7 +283,6 @@ public static void shutdown(BibDatabaseContext bibDatabaseContext, Path backupDi
      *
      * @param backupDir the backup directory
      */
-
     void startBackupTask(Path backupDir, BibDatabaseContext bibDatabaseContext) {
         LOGGER.info("Initializing backup task for directory: {} and file: {}", backupDir, bibDatabaseContext.getDatabasePath().orElseThrow());
         executor.scheduleAtFixedRate(
@@ -292,21 +309,20 @@ void startBackupTask(Path backupDir, BibDatabaseContext bibDatabaseContext) {
      * @throws IOException     if an I/O error occurs
      * @throws GitAPIException if a Git API error occurs
      */
-
     protected void performBackup(Path dbfile, Path backupDir) throws IOException, GitAPIException {
 
         boolean needsCommit = backupGitDiffers(dbfile, backupDir);
 
         if (!needsBackup && !needsCommit) {
-            LOGGER.info("No changes detected, beacuse needsBackup is :{} and needsCommit is :{}", needsBackup, needsCommit);
+            LOGGER.info("No changes detected, beacuse needsBackup is: {} and needsCommit is: {}", needsBackup, needsCommit);
             return;
         }
 
         if (needsBackup) {
-            LOGGER.info("Backup needed, because needsBackup is :{}", needsBackup);
+            LOGGER.info("Backup needed, because needsBackup is: {}", needsBackup);
         } else {
-        LOGGER.info("Backup needed, because needsCommit is :{}", needsCommit);
-    }
+            LOGGER.info("Backup needed, because needsCommit is: {}", needsCommit);
+        }
 
         // Stage the file for commit
         git.add().addFilepattern(".").call();
@@ -316,9 +332,14 @@ protected void performBackup(Path dbfile, Path backupDir) throws IOException, Gi
         RevCommit commit = git.commit()
                               .setMessage("Backup at " + Instant.now().toString())
                               .call();
-        LOGGER.info("Backup committed in :{} with commit ID: {} for the file : {}", backupDir, commit.getName(), bibDatabaseContext.getDatabasePath().orElseThrow());
+        LOGGER.info("Backup committed in: {} with commit ID: {} for the file: {}", backupDir, commit.getName(), bibDatabaseContext.getDatabasePath().orElseThrow());
     }
 
+    /**
+     * Listens for changes in the BibDatabaseContext and sets the needsBackup flag if a change is detected.
+     *
+     * @param event The BibDatabaseContextChangedEvent to listen for.
+     */
     public synchronized void listen(BibDatabaseContextChangedEvent event) {
         if (!event.isFilteredOut()) {
             LOGGER.info("Change detected/LISTENED in file: {}", bibDatabaseContext.getDatabasePath().orElseThrow());
@@ -327,12 +348,14 @@ public synchronized void listen(BibDatabaseContextChangedEvent event) {
     }
 
     /**
-     * Restores the backup from the specified commit.
+     * Restores the backup of the specified database file from the given commit ID.
+     * This method retrieves the content of the file from the specified commit in the Git repository
+     * and rewrites the original file with the retrieved content.
      *
-     * @param backupDir the backup directory
-     * @param objectId the commit ID to restore from
+     * @param dbFile    The path to the database file to be restored.
+     * @param backupDir The backup directory containing the Git repository.
+     * @param objectId  The commit ID from which to restore the file.
      */
-
     public static void restoreBackup(Path dbFile, Path backupDir, ObjectId objectId) {
         try (Repository repository = openGitRepository(backupDir)) {
             // Resolve the filename of dbFile in the repository
@@ -345,7 +368,7 @@ public static void restoreBackup(Path dbFile, Path backupDir, ObjectId objectId)
             LOGGER.info("Restoring file: {}", gitPath);
 
             // Load the content of the file from the specified commit
-            ObjectId fileObjectId = repository.resolve(objectId.getName() + ":" + gitPath);
+            ObjectId fileObjectId = repository.resolve(objectId.getName() + ": " + gitPath);
             if (fileObjectId == null) { // File not found in the commit
                 performBackupNoCommits(dbFile, backupDir);
             }
@@ -363,14 +386,16 @@ public static void restoreBackup(Path dbFile, Path backupDir, ObjectId objectId)
     }
 
     /**
-     * Checks if there are differences between the files in the directory and the last commit.
+     * Checks if there are differences between the current database file and the last committed version in the Git repository.
+     * This method ensures the database file is copied to the backup directory, initializes the Git repository if needed,
+     * and compares the content of the file in the repository with the current file.
      *
-     * @param backupDir the backup directory
-     * @return true if there are differences, false otherwise
-     * @throws IOException if an I/O error occurs
-     * @throws GitAPIException if a Git API error occurs
+     * @param dbFile    The path to the database file to be checked.
+     * @param backupDir The backup directory containing the Git repository.
+     * @return true if there are differences, false otherwise.
+     * @throws IOException     If an I/O error occurs.
+     * @throws GitAPIException If a Git API error occurs.
      */
-
     public static boolean backupGitDiffers(Path dbFile, Path backupDir) throws IOException, GitAPIException {
 
         // Ensure the specific database file is copied to the backup directory
@@ -429,6 +454,14 @@ public static boolean backupGitDiffers(Path dbFile, Path backupDir) throws IOExc
         return false;  // No differences found
     }
 
+    /**
+     * Retrieves the backup file path for the given database file.
+     * This method generates or retrieves a UUID for the file and constructs the backup file path using the UUID.
+     *
+     * @param dbFile    The path to the database file.
+     * @param backupDir The backup directory.
+     * @return The path to the backup file.
+     */
     public static Path getBackupFilePath(Path dbFile, Path backupDir) {
         try {
             String baseName = dbFile.getFileName().toString();
@@ -440,6 +473,15 @@ public static Path getBackupFilePath(Path dbFile, Path backupDir) {
         }
     }
 
+    /**
+     * Writes the backup file content from the specified commit ID to the backup directory.
+     * This method retrieves the content of the file from the specified commit in the Git repository
+     * and rewrites the backup file with the retrieved content.
+     *
+     * @param dbFile    The path to the database file.
+     * @param backupDir The backup directory containing the Git repository.
+     * @param objectId  The commit ID from which to retrieve the file content.
+     */
     public static void writeBackupFileToCommit(Path dbFile, Path backupDir, ObjectId objectId) {
         try (Repository repository = openGitRepository(backupDir)) {
             // Resolve the filename of dbFile in the repository
@@ -452,7 +494,7 @@ public static void writeBackupFileToCommit(Path dbFile, Path backupDir, ObjectId
             LOGGER.info("Restoring file: {}", gitPath);
 
             // Load the content of the file from the specified commit
-            ObjectId fileObjectId = repository.resolve(objectId.getName() + ":" + gitPath);
+            ObjectId fileObjectId = repository.resolve(objectId.getName() + ": " + gitPath);
             if (fileObjectId == null) { // File not found in the commit
                 performBackupNoCommits(dbFile, backupDir);
             }
@@ -470,6 +512,13 @@ public static void writeBackupFileToCommit(Path dbFile, Path backupDir, ObjectId
         }
     }
 
+    /**
+     * Opens the Git repository located in the specified backup directory.
+     *
+     * @param backupDir The backup directory containing the Git repository.
+     * @return The opened Git repository.
+     * @throws IOException If an I/O error occurs.
+     */
     private static Repository openGitRepository(Path backupDir) throws IOException {
         FileRepositoryBuilder builder = new FileRepositoryBuilder();
         // Initialize Git repository from the backup directory
@@ -489,7 +538,6 @@ private static Repository openGitRepository(Path backupDir) throws IOException {
      * @throws IOException if an I/O error occurs
      * @throws GitAPIException if a Git API error occurs
      */
-
     public List<DiffEntry> showDiffers(Path dbFile, Path backupDir, String commitId) throws IOException, GitAPIException {
 
         File repoDir = backupDir.toFile();
@@ -519,7 +567,6 @@ need a class to show the last ten backups indicating: date/ size/ number of entr
      * @throws IOException if an I/O error occurs
      * @throws GitAPIException if a Git API error occurs
      */
-
     public static List<RevCommit> retrieveCommits(Path dbFile, Path backupDir, int n) throws IOException, GitAPIException {
         List<RevCommit> retrievedCommits = new ArrayList<>();
 
@@ -635,6 +682,15 @@ public static List<BackupEntry> retrieveCommitDetails(List<RevCommit> commits, P
         return commitDetails;
     }
 
+    /**
+     * Performs the initial backup by creating the first commit in the Git repository.
+     * This method ensures the Git repository is initialized, stages the database file, and commits it.
+     *
+     * @param dbFile    The path to the database file to be backed up.
+     * @param backupDir The backup directory containing the Git repository.
+     * @throws IOException     If an I/O error occurs.
+     * @throws GitAPIException If a Git API error occurs.
+     */
     public static void performBackupNoCommits(Path dbFile, Path backupDir) throws IOException, GitAPIException {
 
         LOGGER.info("No commits found in the repository. We need a first commit.");

src/main/java/org/jabref/gui/backup/BackupChoiceDialog.java

@@ -36,9 +36,7 @@ public BackupChoiceDialog(Path backupDir, List<BackupEntry> backups) {
         getDialogPane().setMinWidth(450);
         getDialogPane().getButtonTypes().setAll(RESTORE_BACKUP, IGNORE_BACKUP, REVIEW_BACKUP);
 
-        String content = Localization.lang("It looks like JabRef did not shut down cleanly last time the file was used.") + "\n\n" +
-                Localization.lang("Do you want to recover the library from a backup file?");
-
+        String content = Localization.lang("It looks like JabRef did not shut down cleanly last time the file was used.\n\nDo you want to recover the library from a backup file?");
         backupTableView = new TableView<>();
         setupBackupTableView();
         tableData.addAll(backups);