fix some javadoc warnings

Author: vladak

opengrok-indexer/src/main/java/org/opengrok/indexer/history/HistoryGuru.java

@@ -278,22 +278,27 @@ private Annotation getAnnotationFromRepository(File file, @Nullable String rev)
 
     /**
      * Wrapper for {@link #annotate(File, String, boolean)}.
+     * @param file the file to annotate
+     * @param rev the revision to annotate (<code>null</code> means current revision)
+     * @return file annotation, or <code>null</code>
+     * @throws IOException on error
      */
     @Nullable
-    public Annotation annotate(File file, String rev) throws IOException {
+    public Annotation annotate(File file, @Nullable String rev) throws IOException {
         return annotate(file, rev, true);
     }
 
     /**
      * Annotate the specified revision of a file.
      *
      * @param file the file to annotate
-     * @param rev the revision to annotate (<code>null</code> means BASE)
-     * @return file annotation, or <code>null</code> if the <code>HistoryParser</code> does not support annotation
+     * @param rev the revision to annotate (<code>null</code> means current revision)
+     * @param fallback whether to fall back to repository method
+     * @return file annotation, or <code>null</code>
      * @throws IOException if I/O exception occurs
      */
     @Nullable
-    public Annotation annotate(File file, String rev, boolean fallback) throws IOException {
+    public Annotation annotate(File file, @Nullable String rev, boolean fallback) throws IOException {
         Annotation annotation = getAnnotation(file, rev, fallback);
         if (annotation == null) {
             LOGGER.log(Level.FINEST, "no annotation for ''{0}''", file);

opengrok-indexer/src/main/java/org/opengrok/indexer/history/RepositoryFactory.java

@@ -144,10 +144,17 @@ public static Repository getRepository(File file)
     }
 
     /**
-     * Calls {@link #getRepository(File, CommandTimeoutType, boolean)} with {@code file}, {@code interactive}, and {@code false}.
+     * Calls {@link #getRepository(File, CommandTimeoutType, boolean)} with {@code file}, {@code interactive},
+     * and {@code false}.
      * @param file file
      * @param cmdType command timeout type
      * @return repository object
+     * @throws IllegalAccessException on error
+     * @throws InvocationTargetException on error
+     * @throws ForbiddenSymlinkException on error
+     * @throws InstantiationException on error
+     * @throws NoSuchMethodException on error
+     * @throws IOException on error
      */
     public static Repository getRepository(File file, CommandTimeoutType cmdType)
             throws IllegalAccessException, InvocationTargetException, ForbiddenSymlinkException, InstantiationException,

opengrok-indexer/src/main/java/org/opengrok/indexer/index/NumLinesLOCAggregator.java

@@ -52,6 +52,7 @@ public Iterator<AccumulatedNumLinesLOC> iterator() {
      * Registers the specified counts. Values should be negative when deleting a
      * file or when updating a file's analysis to reverse former values before
      * re-registering.
+     * @param counts {@link NumLinesLOC} instance
      */
     public void register(NumLinesLOC counts) {
         File file = new File(counts.getPath());

opengrok-indexer/src/main/java/org/opengrok/indexer/index/NumLinesLOCUtil.java

@@ -35,6 +35,7 @@ public class NumLinesLOCUtil {
 
     /**
      * Reads data, if they exist, from the specified document.
+     * @param doc {@link Document} instance
      * @return a defined instance
      */
     public static NullableNumLinesLOC read(Document doc) {