diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BasePackBitmapIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BasePackBitmapIndex.java
index b78ff2abf..407061fa1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BasePackBitmapIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BasePackBitmapIndex.java
@@ -58,6 +58,7 @@ abstract class BasePackBitmapIndex extends PackBitmapIndex {
 		this.bitmaps = bitmaps;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public EWAHCompressedBitmap getBitmap(AnyObjectId objectId) {
 		StoredBitmap sb = bitmaps.get(objectId);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java
index 88eef4ce8..6ade4386a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java
@@ -59,7 +59,9 @@
 import com.googlecode.javaewah.EWAHCompressedBitmap;
 import com.googlecode.javaewah.IntIterator;
 
-/** A compressed bitmap representation of the entire object graph. */
+/**
+ * A compressed bitmap representation of the entire object graph.
+ */
 public class BitmapIndexImpl implements BitmapIndex {
 	private static final int EXTRA_BITS = 10 * 1024;
 
@@ -85,6 +87,7 @@ PackBitmapIndex getPackBitmapIndex() {
 		return packIndex;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public CompressedBitmap getBitmap(AnyObjectId objectId) {
 		EWAHCompressedBitmap compressed = packIndex.getBitmap(objectId);
@@ -93,6 +96,7 @@ public CompressedBitmap getBitmap(AnyObjectId objectId) {
 		return new CompressedBitmap(compressed, this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public CompressedBitmapBuilder newBitmapBuilder() {
 		return new CompressedBitmapBuilder(this);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteArrayWindow.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteArrayWindow.java
index dc720bc62..338df4a8e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteArrayWindow.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteArrayWindow.java
@@ -63,6 +63,7 @@ final class ByteArrayWindow extends ByteWindow {
 		array = b;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int copy(final int p, final byte[] b, final int o, int n) {
 		n = Math.min(array.length - p, n);
@@ -70,6 +71,7 @@ protected int copy(final int p, final byte[] b, final int o, int n) {
 		return n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int setInput(final int pos, final Inflater inf)
 			throws DataFormatException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteBufferWindow.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteBufferWindow.java
index 05ddd69b3..4dcf133e0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteBufferWindow.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteBufferWindow.java
@@ -65,6 +65,7 @@ final class ByteBufferWindow extends ByteWindow {
 		buffer = b;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int copy(final int p, final byte[] b, final int o, int n) {
 		final ByteBuffer s = buffer.slice();
@@ -89,6 +90,7 @@ void write(PackOutputStream out, long pos, int cnt)
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int setInput(final int pos, final Inflater inf)
 			throws DataFormatException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteWindow.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteWindow.java
index e774a1464..7963ceac4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteWindow.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ByteWindow.java
@@ -66,6 +66,16 @@ abstract class ByteWindow {
 
 	protected final long end;
 
+	/**
+	 * Constructor for ByteWindow.
+	 *
+	 * @param p
+	 *            a {@link org.eclipse.jgit.internal.storage.file.PackFile}.
+	 * @param s
+	 *            where the byte window starts in the pack file
+	 * @param n
+	 *            size of the byte window
+	 */
 	protected ByteWindow(final PackFile p, final long s, final int n) {
 		pack = p;
 		start = s;
@@ -127,6 +137,17 @@ final int setInput(long pos, Inflater inf) throws DataFormatException {
 		return setInput((int) (pos - start), inf);
 	}
 
+	/**
+	 * Set the input
+	 *
+	 * @param pos
+	 *            position
+	 * @param inf
+	 *            an {@link java.util.zip.Inflater} object.
+	 * @return size of the byte window
+	 * @throws java.util.zip.DataFormatException
+	 *             if any.
+	 */
 	protected abstract int setInput(int pos, Inflater inf)
 			throws DataFormatException;
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CachedObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CachedObjectDirectory.java
index ae8260a99..e810ae0e2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CachedObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CachedObjectDirectory.java
@@ -117,11 +117,13 @@ private ObjectIdOwnerMap<UnpackedObjectId> scanLoose() {
 		return m;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// Don't close anything.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectDatabase newCachedDatabase() {
 		return this;
@@ -177,6 +179,7 @@ void resolve(Set<ObjectId> matches, AbbreviatedObjectId id)
 		wrapped.resolve(matches, id);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean has(final AnyObjectId objectId) throws IOException {
 		return has(objectId, null);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
index 2eacb7a79..05cabba83 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
@@ -65,11 +65,13 @@ public class CheckoutEntryImpl implements CheckoutEntry {
 		to = comment.substring(p2 + " to ".length(), p3); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getFromBranch() {
 		return from;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getToBranch() {
 		return to;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileObjectDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileObjectDatabase.java
index 3afc050ba..1f6b20aac 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileObjectDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileObjectDatabase.java
@@ -64,11 +64,13 @@ static enum InsertLooseObjectResult {
 		INSERTED, EXISTS_PACKED, EXISTS_LOOSE, FAILURE;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectReader newReader() {
 		return new WindowCursor(this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectDirectoryInserter newInserter() {
 		return new ObjectDirectoryInserter(this, getConfig());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
index 646feac8c..1a89cff20 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
@@ -116,7 +116,6 @@
  * This class is thread-safe.
  * <p>
  * This implementation only handles a subtly undocumented subset of git features.
- *
  */
 public class FileRepository extends Repository {
 	private static final String UNNAMED = "Unnamed repository; edit this file to name it for gitweb."; //$NON-NLS-1$
@@ -133,8 +132,9 @@ public class FileRepository extends Repository {
 	 * <p>
 	 * The work tree, object directory, alternate object directories and index
 	 * file locations are deduced from the given git directory and the default
-	 * rules by running {@link FileRepositoryBuilder}. This constructor is the
-	 * same as saying:
+	 * rules by running
+	 * {@link org.eclipse.jgit.storage.file.FileRepositoryBuilder}. This
+	 * constructor is the same as saying:
 	 *
 	 * <pre>
 	 * new FileRepositoryBuilder().setGitDir(gitDir).build()
@@ -142,7 +142,7 @@ public class FileRepository extends Repository {
 	 *
 	 * @param gitDir
 	 *            GIT_DIR (the location of the repository metadata).
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository appears to already exist but cannot be
 	 *             accessed.
 	 * @see FileRepositoryBuilder
@@ -156,7 +156,7 @@ public FileRepository(final File gitDir) throws IOException {
 	 *
 	 * @param gitDir
 	 *            GIT_DIR (the location of the repository metadata).
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository appears to already exist but cannot be
 	 *             accessed.
 	 * @see FileRepositoryBuilder
@@ -170,7 +170,7 @@ public FileRepository(final String gitDir) throws IOException {
 	 *
 	 * @param options
 	 *            description of the repository's important paths.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the user configuration file or repository configuration file
 	 *             cannot be accessed.
 	 */
@@ -279,14 +279,10 @@ private void loadRepoConfig() throws IOException {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Create a new Git repository initializing the necessary files and
 	 * directories.
-	 *
-	 * @param bare
-	 *            if true, a bare repository is created.
-	 *
-	 * @throws IOException
-	 *             in case of IO problem
 	 */
 	@Override
 	public void create(boolean bare) throws IOException {
@@ -380,25 +376,27 @@ ConfigConstants.CONFIG_KEY_WORKTREE, getWorkTree()
 	}
 
 	/**
+	 * Get the directory containing the objects owned by this repository
+	 *
 	 * @return the directory containing the objects owned by this repository.
 	 */
 	public File getObjectsDirectory() {
 		return objectDatabase.getDirectory();
 	}
 
-	/** @return the object database storing this repository's data. */
+	/** {@inheritDoc} */
 	@Override
 	public ObjectDirectory getObjectDatabase() {
 		return objectDatabase;
 	}
 
-	/** @return the reference database which stores the reference namespace. */
+	/** {@inheritDoc} */
 	@Override
 	public RefDatabase getRefDatabase() {
 		return refs;
 	}
 
-	/** @return the configuration of this repository. */
+	/** {@inheritDoc} */
 	@Override
 	public FileBasedConfig getConfig() {
 		if (systemConfig.isOutdated()) {
@@ -425,6 +423,7 @@ public FileBasedConfig getConfig() {
 		return repoConfig;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@Nullable
 	public String getGitwebDescription() throws IOException {
@@ -443,6 +442,7 @@ public String getGitwebDescription() throws IOException {
 		return d;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setGitwebDescription(@Nullable String description)
 			throws IOException {
@@ -479,14 +479,14 @@ private File descriptionFile() {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Objects known to exist but not expressed by {@link #getAllRefs()}.
 	 * <p>
 	 * When a repository borrows objects from another repository, it can
 	 * advertise that it safely has that other repository's references, without
-	 * exposing any other details about the other repository.  This may help
-	 * a client trying to push changes avoid pushing more than it needs to.
-	 *
-	 * @return unmodifiable collection of other known objects.
+	 * exposing any other details about the other repository. This may help a
+	 * client trying to push changes avoid pushing more than it needs to.
 	 */
 	@Override
 	public Set<ObjectId> getAdditionalHaves() {
@@ -531,7 +531,7 @@ private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips) {
 	 *
 	 * @param pack
 	 *            path of the pack file to open.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             index file could not be opened, read, or is not recognized as
 	 *             a Git pack file index.
 	 */
@@ -539,6 +539,7 @@ public void openPack(final File pack) throws IOException {
 		objectDatabase.openPack(pack);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void scanForRepoChanges() throws IOException {
 		getRefDatabase().getRefs(ALL); // This will look for changes to refs
@@ -557,18 +558,14 @@ else if (snapshot.isModified(indexFile))
 			notifyIndexChanged();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void notifyIndexChanged() {
 		snapshot = FileSnapshot.save(getIndexFile());
 		fireEvent(new IndexChangedEvent());
 	}
 
-	/**
-	 * @param refName
-	 * @return a {@link ReflogReader} for the supplied refname, or null if the
-	 *         named ref does not exist.
-	 * @throws IOException the ref could not be accessed.
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public ReflogReader getReflogReader(String refName) throws IOException {
 		Ref ref = findRef(refName);
@@ -577,6 +574,7 @@ public ReflogReader getReflogReader(String refName) throws IOException {
 		return null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public AttributesNodeProvider createAttributesNodeProvider() {
 		return new AttributesNodeProviderImpl(this);
@@ -642,6 +640,7 @@ private boolean shouldAutoDetach() {
 				ConfigConstants.CONFIG_KEY_AUTODETACH, true);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void autoGC(ProgressMonitor monitor) {
 		GC gc = new GC(this);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java
index 97f3b573d..2165aa2b7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java
@@ -121,7 +121,6 @@ public static FileSnapshot save(File path) {
 	 *
 	 * @param modified
 	 *            the last modification time of the file
-	 *
 	 * @return the snapshot.
 	 */
 	public static FileSnapshot save(long modified) {
@@ -145,6 +144,8 @@ private FileSnapshot(long read, long modified) {
 	}
 
 	/**
+	 * Get time of last snapshot update
+	 *
 	 * @return time of last snapshot update
 	 */
 	public long lastModified() {
@@ -208,6 +209,7 @@ public boolean equals(FileSnapshot other) {
 		return lastModified == other.lastModified;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object other) {
 		if (other instanceof FileSnapshot)
@@ -215,6 +217,7 @@ public boolean equals(Object other) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		// This is pretty pointless, but override hashCode to ensure that
@@ -223,6 +226,7 @@ public int hashCode() {
 		return (int) lastModified;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		if (this == DIRTY)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index 5f3167176..89801c543 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -124,8 +124,10 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * A garbage collector for git {@link FileRepository}. Instances of this class
- * are not thread-safe. Don't use the same instance from multiple threads.
+ * A garbage collector for git
+ * {@link org.eclipse.jgit.internal.storage.file.FileRepository}. Instances of
+ * this class are not thread-safe. Don't use the same instance from multiple
+ * threads.
  *
  * This class started as a copy of DfsGarbageCollector from Shawn O. Pearce
  * adapted to FileRepositories.
@@ -218,7 +220,8 @@ public GC(FileRepository repo) {
 	}
 
 	/**
-	 * Runs a garbage collector on a {@link FileRepository}. It will
+	 * Runs a garbage collector on a
+	 * {@link org.eclipse.jgit.internal.storage.file.FileRepository}. It will
 	 * <ul>
 	 * <li>pack loose references into packed-refs</li>
 	 * <li>repack all reachable objects into new pack files and delete the old
@@ -235,9 +238,11 @@ public GC(FileRepository repo) {
 	 * return immediately. In this case, errors will not be reported except in
 	 * gc.log.
 	 *
-	 * @return the collection of {@link PackFile}'s which are newly created
-	 * @throws IOException
-	 * @throws ParseException
+	 * @return the collection of
+	 *         {@link org.eclipse.jgit.internal.storage.file.PackFile}'s which
+	 *         are newly created
+	 * @throws java.io.IOException
+	 * @throws java.text.ParseException
 	 *             If the configuration parameter "gc.pruneexpire" couldn't be
 	 *             parsed
 	 */
@@ -475,7 +480,7 @@ private void prunePack(String packName) {
 	 * which can be found in packs. If certain objects can't be pruned (e.g.
 	 * because the filesystem delete operation fails) this is silently ignored.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void prunePacked() throws IOException {
 		ObjectDirectory objdb = repo.getObjectDatabase();
@@ -533,9 +538,8 @@ public void prunePacked() throws IOException {
 	 *
 	 * @param objectsToKeep
 	 *            a set of objects which should explicitly not be pruned
-	 *
-	 * @throws IOException
-	 * @throws ParseException
+	 * @throws java.io.IOException
+	 * @throws java.text.ParseException
 	 *             If the configuration parameter "gc.pruneexpire" couldn't be
 	 *             parsed
 	 */
@@ -782,7 +786,7 @@ private static boolean equals(Ref r1, Ref r2) {
 	/**
 	 * Packs all non-symbolic, loose refs into packed-refs.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void packRefs() throws IOException {
 		Collection<Ref> refs = repo.getRefDatabase().getRefs(Constants.R_REFS).values();
@@ -810,10 +814,10 @@ public void packRefs() throws IOException {
 	 * repacked. All old pack files which existed before are deleted.
 	 *
 	 * @return a collection of the newly created pack files
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             when during reading of refs, index, packfiles, objects,
 	 *             reflog-entries or during writing to the packfiles
-	 *             {@link IOException} occurs
+	 *             {@link java.io.IOException} occurs
 	 */
 	public Collection<PackFile> repack() throws IOException {
 		Collection<PackFile> toBeDeleted = repo.getObjectDatabase().getPacks();
@@ -1312,7 +1316,7 @@ public String toString() {
 	 * Returns information about objects and pack files for a FileRepository.
 	 *
 	 * @return information about objects and pack files for a FileRepository
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public RepoStatistics getStatistics() throws IOException {
 		RepoStatistics ret = new RepoStatistics();
@@ -1357,7 +1361,7 @@ public RepoStatistics getStatistics() throws IOException {
 	/**
 	 * Set the progress monitor used for garbage collection methods.
 	 *
-	 * @param pm
+	 * @param pm a {@link org.eclipse.jgit.lib.ProgressMonitor} object.
 	 * @return this
 	 */
 	public GC setProgressMonitor(ProgressMonitor pm) {
@@ -1399,7 +1403,8 @@ public void setPackExpireAgeMillis(long packExpireAgeMillis) {
 	 * "git gc --aggressive"
 	 *
 	 * @param pconfig
-	 *            the {@link PackConfig} used when writing packs
+	 *            the {@link org.eclipse.jgit.storage.pack.PackConfig} used when
+	 *            writing packs
 	 */
 	public void setPackConfig(PackConfig pconfig) {
 		this.pconfig = pconfig;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GlobalAttributesNode.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GlobalAttributesNode.java
index 454d3bff6..2f5de049f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GlobalAttributesNode.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GlobalAttributesNode.java
@@ -51,20 +51,27 @@
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.FS;
 
-/** Attribute node loaded from global system-wide file. */
+/**
+ * Attribute node loaded from global system-wide file.
+ */
 public class GlobalAttributesNode extends AttributesNode {
 	final Repository repository;
 
 	/**
+	 * Constructor for GlobalAttributesNode.
+	 *
 	 * @param repository
+	 *            the {@link org.eclipse.jgit.lib.Repository}.
 	 */
 	public GlobalAttributesNode(Repository repository) {
 		this.repository = repository;
 	}
 
 	/**
+	 * Load the attributes node
+	 *
 	 * @return the attributes node
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public AttributesNode load() throws IOException {
 		AttributesNode r = new AttributesNode();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
index 3f82e2a20..cd0937415 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
@@ -51,20 +51,27 @@
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.FS;
 
-/** Attribute node loaded from the $GIT_DIR/info/attributes file. */
+/**
+ * Attribute node loaded from the $GIT_DIR/info/attributes file.
+ */
 public class InfoAttributesNode extends AttributesNode {
 	final Repository repository;
 
 	/**
+	 * Constructor for InfoAttributesNode.
+	 *
 	 * @param repository
+	 *            the {@link org.eclipse.jgit.lib.Repository}.
 	 */
 	public InfoAttributesNode(Repository repository) {
 		this.repository = repository;
 	}
 
 	/**
+	 * Load the attributes node
+	 *
 	 * @return the attributes node
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public AttributesNode load() throws IOException {
 		AttributesNode r = new AttributesNode();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LargePackedWholeObject.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LargePackedWholeObject.java
index 4d6e4dd58..229d3ff24 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LargePackedWholeObject.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LargePackedWholeObject.java
@@ -77,21 +77,25 @@ class LargePackedWholeObject extends ObjectLoader {
 		this.db = db;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getType() {
 		return type;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getSize() {
 		return size;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isLarge() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public byte[] getCachedBytes() throws LargeObjectException {
 		try {
@@ -103,6 +107,7 @@ public byte[] getCachedBytes() throws LargeObjectException {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectStream openStream() throws MissingObjectException, IOException {
 		WindowCursor wc = new WindowCursor(db);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LazyObjectIdSetFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LazyObjectIdSetFile.java
index 1e2617c0e..3d0e9c718 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LazyObjectIdSetFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LazyObjectIdSetFile.java
@@ -57,7 +57,9 @@
 import org.eclipse.jgit.lib.ObjectIdOwnerMap;
 import org.eclipse.jgit.lib.ObjectIdSet;
 
-/** Lazily loads a set of ObjectIds, one per line. */
+/**
+ * Lazily loads a set of ObjectIds, one per line.
+ */
 public class LazyObjectIdSetFile implements ObjectIdSet {
 	private final File src;
 	private ObjectIdOwnerMap<Entry> set;
@@ -72,6 +74,7 @@ public LazyObjectIdSetFile(File src) {
 		this.src = src;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean contains(AnyObjectId objectId) {
 		if (set == null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalCachedPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalCachedPack.java
index 74453ee4b..289d89d69 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalCachedPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalCachedPack.java
@@ -71,6 +71,7 @@ class LocalCachedPack extends CachedPack {
 		this.packs = packs.toArray(new PackFile[packs.size()]);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getObjectCount() throws IOException {
 		long cnt = 0;
@@ -85,6 +86,7 @@ void copyAsIs(PackOutputStream out, WindowCursor wc)
 			pack.copyPackAsIs(out, wc);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean hasObject(ObjectToPack obj, StoredObjectRepresentation rep) {
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectRepresentation.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectRepresentation.java
index a42e6797d..35f97735c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectRepresentation.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectRepresentation.java
@@ -92,11 +92,13 @@ static LocalObjectRepresentation newDelta(PackFile f, long p, long n,
 
 	private ObjectId baseId;
 
+	/** {@inheritDoc} */
 	@Override
 	public int getWeight() {
 		return (int) Math.min(length, Integer.MAX_VALUE);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getDeltaBase() {
 		if (baseId == null && getFormat() == PACK_DELTA) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectToPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectToPack.java
index fafe1321e..55eeb95ce 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectToPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LocalObjectToPack.java
@@ -62,12 +62,14 @@ class LocalObjectToPack extends ObjectToPack {
 		super(src, type);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void clearReuseAsIs() {
 		super.clearReuseAsIs();
 		pack = null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void select(StoredObjectRepresentation ref) {
 		LocalObjectRepresentation ptr = (LocalObjectRepresentation) ref;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
index 9b1fe8ce9..3460913e9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
@@ -57,7 +57,6 @@
 import java.nio.file.StandardCopyOption;
 import java.text.MessageFormat;
 
-import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -81,10 +80,12 @@ public class LockFile {
 	 * Unlock the given file.
 	 * <p>
 	 * This method can be used for recovering from a thrown
-	 * {@link LockFailedException} . This method does not validate that the lock
-	 * is or is not currently held before attempting to unlock it.
+	 * {@link org.eclipse.jgit.errors.LockFailedException} . This method does
+	 * not validate that the lock is or is not currently held before attempting
+	 * to unlock it.
 	 *
 	 * @param file
+	 *            a {@link java.io.File} object.
 	 * @return true if unlocked, false if unlocking failed
 	 */
 	public static boolean unlock(final File file) {
@@ -138,7 +139,9 @@ public boolean accept(File dir, String name) {
 	 * @param fs
 	 *            the file system abstraction which will be necessary to perform
 	 *            certain file system operations.
-	 * @deprecated use {@link LockFile#LockFile(File)} instead
+	 * @deprecated use
+	 *             {@link org.eclipse.jgit.internal.storage.file.LockFile#LockFile(File)}
+	 *             instead
 	 */
 	@Deprecated
 	public LockFile(final File f, final FS fs) {
@@ -162,7 +165,7 @@ public LockFile(final File f) {
 	 *
 	 * @return true if the lock is now held by the caller; false if it is held
 	 *         by someone else.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the temporary output file could not be created. The caller
 	 *             does not hold the lock.
 	 */
@@ -185,7 +188,7 @@ public boolean lock() throws IOException {
 	 *
 	 * @return true if the lock is now held by the caller; false if it is held
 	 *         by someone else.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the temporary output file could not be created. The caller
 	 *             does not hold the lock.
 	 */
@@ -206,12 +209,12 @@ public boolean lockForAppend() throws IOException {
 	 * This method does nothing if the current file does not exist, or exists
 	 * but is empty.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the temporary file could not be written, or a read error
 	 *             occurred while reading from the current file. The lock is
 	 *             released before throwing the underlying IO exception to the
 	 *             caller.
-	 * @throws RuntimeException
+	 * @throws java.lang.RuntimeException
 	 *             the temporary file could not be written. The lock is released
 	 *             before throwing the underlying exception to the caller.
 	 */
@@ -264,10 +267,10 @@ public void copyCurrentContent() throws IOException {
 	 * @param id
 	 *            the id to store in the file. The id will be written in hex,
 	 *            followed by a sole LF.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the temporary file could not be written. The lock is released
 	 *             before throwing the underlying IO exception to the caller.
-	 * @throws RuntimeException
+	 * @throws java.lang.RuntimeException
 	 *             the temporary file could not be written. The lock is released
 	 *             before throwing the underlying exception to the caller.
 	 */
@@ -285,10 +288,10 @@ public void write(final ObjectId id) throws IOException {
 	 *            the bytes to store in the temporary file. No additional bytes
 	 *            are added, so if the file must end with an LF it must appear
 	 *            at the end of the byte array.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the temporary file could not be written. The lock is released
 	 *             before throwing the underlying IO exception to the caller.
-	 * @throws RuntimeException
+	 * @throws java.lang.RuntimeException
 	 *             the temporary file could not be written. The lock is released
 	 *             before throwing the underlying exception to the caller.
 	 */
@@ -394,7 +397,8 @@ public void setNeedStatInformation(final boolean on) {
 	}
 
 	/**
-	 * Request that {@link #commit()} remember the {@link FileSnapshot}.
+	 * Request that {@link #commit()} remember the
+	 * {@link org.eclipse.jgit.internal.storage.file.FileSnapshot}.
 	 *
 	 * @param on
 	 *            true if the commit method must remember the FileSnapshot.
@@ -420,7 +424,7 @@ public void setFSync(final boolean on) {
 	 * method sleeps until it can force the new lock file's modification date to
 	 * be later than the target file.
 	 *
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             the thread was interrupted before the last modified date of
 	 *             the lock file was different from the last modified date of
 	 *             the target file.
@@ -443,7 +447,7 @@ public void waitForStatChange() throws InterruptedException {
 	 * @return true if the commit was successful and the file contains the new
 	 *         data; false if the commit failed and the file remains with the
 	 *         old data.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             the lock is not held.
 	 */
 	public boolean commit() {
@@ -477,7 +481,11 @@ public long getCommitLastModified() {
 		return commitSnapshot.lastModified();
 	}
 
-	/** @return get the {@link FileSnapshot} just before commit. */
+	/**
+	 * Get the {@link FileSnapshot} just before commit.
+	 *
+	 * @return get the {@link FileSnapshot} just before commit.
+	 */
 	public FileSnapshot getCommitSnapshot() {
 		return commitSnapshot;
 	}
@@ -517,6 +525,7 @@ public void unlock() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
index 068db6115..3e2fd82ce 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
@@ -91,12 +91,12 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Traditional file system based {@link ObjectDatabase}.
+ * Traditional file system based {@link org.eclipse.jgit.lib.ObjectDatabase}.
  * <p>
  * This is the classical object database representation for a Git repository,
  * where objects are stored loose by hashing them into directories by their
- * {@link ObjectId}, or are stored in compressed containers known as
- * {@link PackFile}s.
+ * {@link org.eclipse.jgit.lib.ObjectId}, or are stored in compressed containers
+ * known as {@link org.eclipse.jgit.internal.storage.file.PackFile}s.
  * <p>
  * Optionally an object database can reference one or more alternates; other
  * ObjectDatabase instances that are searched in addition to the current
@@ -161,7 +161,7 @@ public class ObjectDirectory extends FileObjectDatabase {
 	 * @param shallowFile
 	 *            file which contains IDs of shallow commits, null if shallow
 	 *            commits handling should be turned off
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an alternate object cannot be opened.
 	 */
 	public ObjectDirectory(final Config cfg, final File dir,
@@ -188,15 +188,15 @@ public ObjectDirectory(final Config cfg, final File dir,
 		}
 	}
 
-	/**
-	 * @return the location of the <code>objects</code> directory.
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public final File getDirectory() {
 		return objects;
 	}
 
 	/**
+	 * <p>Getter for the field <code>packDirectory</code>.</p>
+	 *
 	 * @return the location of the <code>pack</code> directory.
 	 * @since 4.10
 	 */
@@ -205,17 +205,21 @@ public final File getPackDirectory() {
 	}
 
 	/**
+	 * <p>Getter for the field <code>preservedDirectory</code>.</p>
+	 *
 	 * @return the location of the <code>preserved</code> directory.
 	 */
 	public final File getPreservedDirectory() {
 		return preservedDirectory;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean exists() {
 		return fs.exists(objects);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void create() throws IOException {
 		FileUtils.mkdirs(objects);
@@ -223,6 +227,7 @@ public void create() throws IOException {
 		FileUtils.mkdir(packDirectory);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectDirectoryInserter newInserter() {
 		return new ObjectDirectoryInserter(this, config);
@@ -238,6 +243,7 @@ public PackInserter newPackInserter() {
 		return new PackInserter(this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		unpackedObjectCache.clear();
@@ -256,13 +262,7 @@ public void close() {
 		}
 	}
 
-	/**
-	 * @return unmodifiable collection of all known pack files local to this
-	 *         directory. Most recent packs are presented first. Packs most
-	 *         likely to contain more recent objects appear before packs
-	 *         containing objects referenced by commits further back in the
-	 *         history of the repository.
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Collection<PackFile> getPacks() {
 		PackList list = packList.get();
@@ -273,14 +273,9 @@ public Collection<PackFile> getPacks() {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Add a single existing pack to the list of available pack files.
-	 *
-	 * @param pack
-	 *            path of the pack file to open.
-	 * @return the pack that was opened and added to the database.
-	 * @throws IOException
-	 *             index file could not be opened, read, or is not recognized as
-	 *             a Git pack file index.
 	 */
 	@Override
 	public PackFile openPack(final File pack)
@@ -307,11 +302,13 @@ public PackFile openPack(final File pack)
 		return res;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return "ObjectDirectory[" + getDirectory() + "]"; //$NON-NLS-1$ //$NON-NLS-2$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean has(AnyObjectId objectId) {
 		return unpackedObjectCache.isUnpacked(objectId)
@@ -1066,11 +1063,9 @@ private AlternateHandle openAlternate(File objdir) throws IOException {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Compute the location of a loose object file.
-	 *
-	 * @param objectId
-	 *            identity of the loose object to map to the directory.
-	 * @return location of the object, if it were to exist as a loose object.
 	 */
 	@Override
 	public File fileFor(AnyObjectId objectId) {
@@ -1155,6 +1150,7 @@ void close() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectDatabase newCachedDatabase() {
 		return newCachedFileObjectDatabase();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryInserter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryInserter.java
index aa435bf67..e06f72167 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryInserter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryInserter.java
@@ -83,6 +83,7 @@ class ObjectDirectoryInserter extends ObjectInserter {
 		config = cfg.get(WriteConfig.KEY);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId insert(int type, byte[] data, int off, int len)
 			throws IOException {
@@ -114,6 +115,7 @@ private ObjectId insert(
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId insert(final int type, long len, final InputStream is)
 			throws IOException {
@@ -166,21 +168,25 @@ private ObjectId insertOneObject(
 				.format(JGitText.get().unableToCreateNewObject, dst));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PackParser newPackParser(InputStream in) throws IOException {
 		return new ObjectDirectoryPackParser(db, in);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectReader newReader() {
 		return new WindowCursor(db, this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		// Do nothing. Loose objects are immediately visible.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (deflate != null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
index 2e6c245ea..5dcba6001 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
@@ -64,7 +64,6 @@
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig;
 import org.eclipse.jgit.lib.ObjectId;
-import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.transport.PackParser;
 import org.eclipse.jgit.transport.PackedObjectInfo;
@@ -72,10 +71,11 @@
 import org.eclipse.jgit.util.NB;
 
 /**
- * Consumes a pack stream and stores as a pack file in {@link ObjectDirectory}.
+ * Consumes a pack stream and stores as a pack file in
+ * {@link org.eclipse.jgit.internal.storage.file.ObjectDirectory}.
  * <p>
  * To obtain an instance of a parser, applications should use
- * {@link ObjectInserter#newPackParser(InputStream)}.
+ * {@link org.eclipse.jgit.lib.ObjectInserter#newPackParser(InputStream)}.
  */
 public class ObjectDirectoryPackParser extends PackParser {
 	private final FileObjectDatabase db;
@@ -158,7 +158,7 @@ public void setKeepEmpty(final boolean empty) {
 	}
 
 	/**
-	 * Get the imported {@link PackFile}.
+	 * Get the imported {@link org.eclipse.jgit.internal.storage.file.PackFile}.
 	 * <p>
 	 * This method is supplied only to support testing; applications shouldn't
 	 * be using it directly to access the imported data.
@@ -169,6 +169,7 @@ public PackFile getPackFile() {
 		return newPack;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getPackSize() {
 		if (newPack == null)
@@ -184,6 +185,7 @@ public long getPackSize() {
 		return size;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 			throws IOException {
@@ -218,34 +220,40 @@ public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onPackHeader(long objectCount) throws IOException {
 		// Ignored, the count is not required.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onBeginWholeObject(long streamPosition, int type,
 			long inflatedSize) throws IOException {
 		crc.reset();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndWholeObject(PackedObjectInfo info) throws IOException {
 		info.setCRC((int) crc.getValue());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onBeginOfsDelta(long streamPosition,
 			long baseStreamPosition, long inflatedSize) throws IOException {
 		crc.reset();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onBeginRefDelta(long streamPosition, AnyObjectId baseId,
 			long inflatedSize) throws IOException {
 		crc.reset();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected UnresolvedDelta onEndDelta() throws IOException {
 		UnresolvedDelta delta = new UnresolvedDelta();
@@ -253,30 +261,35 @@ protected UnresolvedDelta onEndDelta() throws IOException {
 		return delta;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onInflatedObjectData(PackedObjectInfo obj, int typeCode,
 			byte[] data) throws IOException {
 		// ObjectDirectory ignores this event.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onObjectHeader(Source src, byte[] raw, int pos, int len)
 			throws IOException {
 		crc.update(raw, pos, len);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onObjectData(Source src, byte[] raw, int pos, int len)
 			throws IOException {
 		crc.update(raw, pos, len);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onStoreStream(byte[] raw, int pos, int len)
 			throws IOException {
 		out.write(raw, pos, len);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onPackFooter(byte[] hash) throws IOException {
 		packEnd = out.getFilePointer();
@@ -285,6 +298,7 @@ protected void onPackFooter(byte[] hash) throws IOException {
 		packHash = hash;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected ObjectTypeAndSize seekDatabase(UnresolvedDelta delta,
 			ObjectTypeAndSize info) throws IOException {
@@ -293,6 +307,7 @@ protected ObjectTypeAndSize seekDatabase(UnresolvedDelta delta,
 		return readObjectHeader(info);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected ObjectTypeAndSize seekDatabase(PackedObjectInfo obj,
 			ObjectTypeAndSize info) throws IOException {
@@ -301,11 +316,13 @@ protected ObjectTypeAndSize seekDatabase(PackedObjectInfo obj,
 		return readObjectHeader(info);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int readDatabase(byte[] dst, int pos, int cnt) throws IOException {
 		return out.read(dst, pos, cnt);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean checkCRC(int oldCRC) {
 		return oldCRC == (int) crc.getValue();
@@ -323,6 +340,7 @@ private void cleanupTemporaryFiles() {
 			tmpPack.deleteOnExit();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean onAppendBase(final int typeCode, final byte[] data,
 			final PackedObjectInfo info) throws IOException {
@@ -365,6 +383,7 @@ protected boolean onAppendBase(final int typeCode, final byte[] data,
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndThinPack() throws IOException {
 		final byte[] buf = buffer();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndex.java
index 7fb8e6d64..181951c65 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndex.java
@@ -58,11 +58,11 @@
 
 /**
  * Logical representation of the bitmap data stored in the pack index.
- * {@link ObjectId}s are encoded as a single integer in the range [0,
- * {@link #getObjectCount()}). Compressed bitmaps are available at certain
- * {@code ObjectId}s, which represent all of the objects reachable from that
- * {@code ObjectId} (include the {@code ObjectId} itself). The meaning of the
- * positions in the bitmaps can be decoded using {@link #getObject(int)} and
+ * {@link org.eclipse.jgit.lib.ObjectId}s are encoded as a single integer in the
+ * range [0, {@link #getObjectCount()}). Compressed bitmaps are available at
+ * certain {@code ObjectId}s, which represent all of the objects reachable from
+ * that {@code ObjectId} (include the {@code ObjectId} itself). The meaning of
+ * the positions in the bitmaps can be decoded using {@link #getObject(int)} and
  * {@link #ofObjectType(EWAHCompressedBitmap, int)}. Furthermore,
  * {@link #findPosition(AnyObjectId)} can be used to build other bitmaps that a
  * compatible with the encoded bitmaps available from the index.
@@ -85,7 +85,7 @@ public abstract class PackBitmapIndex {
 	 * @param reverseIndex
 	 *            the pack reverse index for the corresponding pack file.
 	 * @return a copy of the index in-memory.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be read.
 	 * @throws CorruptObjectException
 	 *             the stream does not contain a valid pack bitmap index.
@@ -128,7 +128,7 @@ public static PackBitmapIndex open(
 	 * @param reverseIndex
 	 *            the pack reverse index for the corresponding pack file.
 	 * @return a copy of the index in-memory.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be read.
 	 * @throws CorruptObjectException
 	 *             the stream does not contain a valid pack bitmap index.
@@ -157,7 +157,7 @@ public static PackBitmapIndex read(
 	 * @param position
 	 *            the id for which the object will be found.
 	 * @return the ObjectId.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             when the item is not found.
 	 */
 	public abstract ObjectId getObject(int position) throws IllegalArgumentException;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexBuilder.java
index bfd60fc53..70eb10ea8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexBuilder.java
@@ -64,7 +64,8 @@
 import com.googlecode.javaewah.EWAHCompressedBitmap;
 
 /**
- * Helper for constructing {@link PackBitmapIndex}es.
+ * Helper for constructing
+ * {@link org.eclipse.jgit.internal.storage.file.PackBitmapIndex}es.
  */
 public class PackBitmapIndexBuilder extends BasePackBitmapIndex {
 	private static final int MAX_XOR_OFFSET_SEARCH = 10;
@@ -145,7 +146,11 @@ public int compare(ObjectToPack a, ObjectToPack b) {
 		}
 	}
 
-	/** @return set of objects included in the pack. */
+	/**
+	 * Get set of objects included in the pack.
+	 *
+	 * @return set of objects included in the pack.
+	 */
 	public ObjectIdOwnerMap<ObjectIdOwnerMap.Entry> getObjectSet() {
 		ObjectIdOwnerMap<ObjectIdOwnerMap.Entry> r = new ObjectIdOwnerMap<>();
 		for (PositionEntry e : byOffset) {
@@ -197,6 +202,7 @@ public void addBitmap(
 		byAddOrder.add(result);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public EWAHCompressedBitmap ofObjectType(
 			EWAHCompressedBitmap bitmap, int type) {
@@ -213,6 +219,7 @@ public EWAHCompressedBitmap ofObjectType(
 		throw new IllegalArgumentException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int findPosition(AnyObjectId objectId) {
 		PositionEntry entry = positionEntries.get(objectId);
@@ -221,6 +228,7 @@ public int findPosition(AnyObjectId objectId) {
 		return entry.offsetPosition;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getObject(int position) throws IllegalArgumentException {
 		ObjectId objectId = byOffset.get(position);
@@ -229,48 +237,76 @@ public ObjectId getObject(int position) throws IllegalArgumentException {
 		return objectId;
 	}
 
-	/** @return the commit object bitmap. */
+	/**
+	 * Get the commit object bitmap.
+	 *
+	 * @return the commit object bitmap.
+	 */
 	public EWAHCompressedBitmap getCommits() {
 		return commits;
 	}
 
-	/** @return the tree object bitmap. */
+	/**
+	 * Get the tree object bitmap.
+	 *
+	 * @return the tree object bitmap.
+	 */
 	public EWAHCompressedBitmap getTrees() {
 		return trees;
 	}
 
-	/** @return the blob object bitmap. */
+	/**
+	 * Get the blob object bitmap.
+	 *
+	 * @return the blob object bitmap.
+	 */
 	public EWAHCompressedBitmap getBlobs() {
 		return blobs;
 	}
 
-	/** @return the tag object bitmap. */
+	/**
+	 * Get the tag object bitmap.
+	 *
+	 * @return the tag object bitmap.
+	 */
 	public EWAHCompressedBitmap getTags() {
 		return tags;
 	}
 
-	/** @return the index storage options. */
+	/**
+	 * Get the index storage options.
+	 *
+	 * @return the index storage options.
+	 */
 	public int getOptions() {
 		return PackBitmapIndexV1.OPT_FULL;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getBitmapCount() {
 		return getBitmaps().size();
 	}
 
-	/** Removes all the bitmaps entries added. */
+	/**
+	 * Remove all the bitmaps entries added.
+	 */
 	public void clearBitmaps() {
 		byAddOrder.clear();
 		getBitmaps().clear();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getObjectCount() {
 		return byOffset.size();
 	}
 
-	/** @return an iterator over the xor compressed entries. */
+	/**
+	 * Get an iterator over the xor compressed entries.
+	 *
+	 * @return an iterator over the xor compressed entries.
+	 */
 	public Iterable<StoredEntry> getCompressedBitmaps() {
 		// Add order is from oldest to newest. The reverse add order is the
 		// output order.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
index 9a8c2752d..c04c90f22 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
@@ -116,27 +116,32 @@ private PackBitmapIndexRemapper(
 					oldPackIndex.getObject(pos));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int findPosition(AnyObjectId objectId) {
 		return newPackIndex.findPosition(objectId);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getObject(int position) throws IllegalArgumentException {
 		return newPackIndex.getObject(position);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getObjectCount() {
 		return newPackIndex.getObjectCount();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public EWAHCompressedBitmap ofObjectType(
 			EWAHCompressedBitmap bitmap, int type) {
 		return newPackIndex.ofObjectType(bitmap, type);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<Entry> iterator() {
 		if (oldPackIndex == null)
@@ -173,6 +178,7 @@ public void remove() {
 		};
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public EWAHCompressedBitmap getBitmap(AnyObjectId objectId) {
 		EWAHCompressedBitmap bitmap = newPackIndex.getBitmap(objectId);
@@ -214,6 +220,7 @@ public int getFlags() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getBitmapCount() {
 		// The count is only useful for the end index, not the remapper.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexV1.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexV1.java
index 9d2c70b4c..b172ca4af 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexV1.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexV1.java
@@ -175,6 +175,7 @@ class PackBitmapIndexV1 extends BasePackBitmapIndex {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int findPosition(AnyObjectId objectId) {
 		long offset = packIndex.findOffset(objectId);
@@ -183,6 +184,7 @@ public int findPosition(AnyObjectId objectId) {
 		return reverseIndex.findPostion(offset);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getObject(int position) throws IllegalArgumentException {
 		ObjectId objectId = reverseIndex.findObjectByPosition(position);
@@ -191,11 +193,13 @@ public ObjectId getObject(int position) throws IllegalArgumentException {
 		return objectId;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getObjectCount() {
 		return (int) packIndex.getObjectCount();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public EWAHCompressedBitmap ofObjectType(
 			EWAHCompressedBitmap bitmap, int type) {
@@ -212,11 +216,13 @@ public EWAHCompressedBitmap ofObjectType(
 		throw new IllegalArgumentException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getBitmapCount() {
 		return bitmaps.size();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object o) {
 		// TODO(cranger): compare the pack checksum?
@@ -225,6 +231,7 @@ public boolean equals(Object o) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		return getPackIndex().hashCode();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexWriterV1.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexWriterV1.java
index f8f02e95e..d0c84da78 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexWriterV1.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexWriterV1.java
@@ -89,7 +89,7 @@ public PackBitmapIndexWriterV1(final OutputStream dst) {
 	 * @param packDataChecksum
 	 *            checksum signature of the entire pack data content. This is
 	 *            traditionally the last 20 bytes of the pack file's own stream.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream, or this
 	 *             index format cannot store the object data supplied.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
index 0611d3e85..febbb9602 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
@@ -201,20 +201,30 @@ private synchronized PackIndex idx() throws IOException {
 		return loadedIdx;
 	}
 
-	/** @return the File object which locates this pack on disk. */
+	/**
+	 * Get the File object which locates this pack on disk.
+	 *
+	 * @return the File object which locates this pack on disk.
+	 */
 	public File getPackFile() {
 		return packFile;
 	}
 
 	/**
+	 * Get the index for this pack file.
+	 *
 	 * @return the index for this pack file.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public PackIndex getIndex() throws IOException {
 		return idx();
 	}
 
-	/** @return name extracted from {@code pack-*.pack} pattern. */
+	/**
+	 * Get name extracted from {@code pack-*.pack} pattern.
+	 *
+	 * @return name extracted from {@code pack-*.pack} pattern.
+	 */
 	public String getPackName() {
 		String name = packName;
 		if (name == null) {
@@ -238,7 +248,7 @@ public String getPackName() {
 	 * @param id
 	 *            the object to look for. Must not be null.
 	 * @return true if the object is in this pack; false otherwise.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the index file cannot be loaded into memory.
 	 */
 	public boolean hasObject(final AnyObjectId id) throws IOException {
@@ -292,6 +302,8 @@ public void close() {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Provide iterator over entries in associated pack index, that should also
 	 * exist in this pack file. Objects returned by such iterator are mutable
 	 * during iteration.
@@ -299,8 +311,6 @@ public void close() {
 	 * Iterator returns objects in SHA-1 lexicographical order.
 	 * </p>
 	 *
-	 * @return iterator over entries of associated pack index
-	 *
 	 * @see PackIndex#iterator()
 	 */
 	@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndex.java
index 2252778db..a7000e89d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndex.java
@@ -66,7 +66,8 @@
 import org.eclipse.jgit.util.NB;
 
 /**
- * Access path to locate objects by {@link ObjectId} in a {@link PackFile}.
+ * Access path to locate objects by {@link org.eclipse.jgit.lib.ObjectId} in a
+ * {@link org.eclipse.jgit.internal.storage.file.PackFile}.
  * <p>
  * Indexes are strictly redundant information in that we can rebuild all of the
  * data held in the index file from the on disk representation of the pack file
@@ -89,7 +90,7 @@ public abstract class PackIndex
 	 * @return access implementation for the requested file.
 	 * @throws FileNotFoundException
 	 *             the file does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file exists but could not be read due to security errors,
 	 *             unrecognized data version, or unexpected data corruption.
 	 */
@@ -124,9 +125,9 @@ public static PackIndex open(final File idxFile) throws IOException {
 	 *            buffered as some small IOs are performed against the stream.
 	 *            The caller is responsible for closing the stream.
 	 * @return a copy of the index in-memory.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be read.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             the stream does not contain a valid pack index.
 	 */
 	public static PackIndex read(InputStream fd) throws IOException,
@@ -167,12 +168,15 @@ public boolean hasObject(final AnyObjectId id) {
 		return findOffset(id) != -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean contains(AnyObjectId id) {
 		return findOffset(id) != -1;
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Provide iterator that gives access to index entries. Note, that iterator
 	 * returns reference to mutable object, the same reference in each call -
 	 * for performance reason. If client needs immutable objects, it must copy
@@ -180,8 +184,6 @@ public boolean contains(AnyObjectId id) {
 	 * <p>
 	 * Iterator returns objects in SHA-1 lexicographical order.
 	 * </p>
-	 *
-	 * @return iterator over pack index entries
 	 */
 	@Override
 	public abstract Iterator<MutableEntry> iterator();
@@ -218,7 +220,8 @@ public boolean contains(AnyObjectId id) {
 	 * @param nthPosition
 	 *            position within the traversal of {@link #iterator()} that the
 	 *            caller needs the object for. The first returned
-	 *            {@link MutableEntry} is 0, the second is 1, etc.
+	 *            {@link org.eclipse.jgit.internal.storage.file.PackIndex.MutableEntry}
+	 *            is 0, the second is 1, etc.
 	 * @return the ObjectId for the corresponding entry.
 	 */
 	public abstract ObjectId getObjectId(long nthPosition);
@@ -239,8 +242,10 @@ public boolean contains(AnyObjectId id) {
 	 * @param nthPosition
 	 *            unsigned 32 bit position within the traversal of
 	 *            {@link #iterator()} that the caller needs the object for. The
-	 *            first returned {@link MutableEntry} is 0, the second is 1,
-	 *            etc. Positions past 2**31-1 are negative, but still valid.
+	 *            first returned
+	 *            {@link org.eclipse.jgit.internal.storage.file.PackIndex.MutableEntry}
+	 *            is 0, the second is 1, etc. Positions past 2**31-1 are
+	 *            negative, but still valid.
 	 * @return the ObjectId for the corresponding entry.
 	 */
 	public final ObjectId getObjectId(final int nthPosition) {
@@ -282,9 +287,9 @@ public final ObjectId getObjectId(final int nthPosition) {
 	 * @param objId
 	 *            id of object to look for
 	 * @return CRC32 checksum of specified object (at 32 less significant bits)
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             when requested ObjectId was not found in this index
-	 * @throws UnsupportedOperationException
+	 * @throws java.lang.UnsupportedOperationException
 	 *             when this index doesn't support CRC32 checksum
 	 */
 	public abstract long findCRC32(AnyObjectId objId)
@@ -308,7 +313,7 @@ public abstract long findCRC32(AnyObjectId objId)
 	 * @param matchLimit
 	 *            maximum number of results to return. At most this many
 	 *            ObjectIds should be added to matches before returning.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the index cannot be read.
 	 */
 	public abstract void resolve(Set<ObjectId> matches, AbbreviatedObjectId id,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV1.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV1.java
index 8a0845624..8ea31e4fa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV1.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV1.java
@@ -103,11 +103,13 @@ class PackIndexV1 extends PackIndex {
 		IO.readFully(fd, packChecksum, 0, packChecksum.length);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getObjectCount() {
 		return objectCnt;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getOffset64Count() {
 		long n64 = 0;
@@ -140,6 +142,7 @@ private int getLevelTwo(final long nthPosition, final int levelOne) {
 		return (int) (nthPosition - base);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getObjectId(final long nthPosition) {
 		final int levelOne = findLevelOne(nthPosition);
@@ -156,6 +159,7 @@ long getOffset(long nthPosition) {
 		return NB.decodeUInt32(idxdata[levelOne], p);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long findOffset(final AnyObjectId objId) {
 		final int levelOne = objId.getFirstByte();
@@ -182,21 +186,25 @@ else if (cmp == 0) {
 		return -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long findCRC32(AnyObjectId objId) {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean hasCRC32Support() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<MutableEntry> iterator() {
 		return new IndexV1Iterator();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void resolve(Set<ObjectId> matches, AbbreviatedObjectId id,
 			int matchLimit) throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV2.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV2.java
index 5c2986a04..9f6201f9a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV2.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexV2.java
@@ -164,11 +164,13 @@ class PackIndexV2 extends PackIndex {
 		IO.readFully(fd, packChecksum, 0, packChecksum.length);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getObjectCount() {
 		return objectCnt;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getOffset64Count() {
 		return offset64.length / 8;
@@ -196,6 +198,7 @@ private int getLevelTwo(final long nthPosition, final int levelOne) {
 		return (int) (nthPosition - base);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getObjectId(final long nthPosition) {
 		final int levelOne = findLevelOne(nthPosition);
@@ -204,6 +207,7 @@ public ObjectId getObjectId(final long nthPosition) {
 		return ObjectId.fromRaw(names[levelOne], p4 + p); // p * 5
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getOffset(final long nthPosition) {
 		final int levelOne = findLevelOne(nthPosition);
@@ -211,6 +215,7 @@ public long getOffset(final long nthPosition) {
 		return getOffset(levelOne, levelTwo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long findOffset(final AnyObjectId objId) {
 		final int levelOne = objId.getFirstByte();
@@ -227,6 +232,7 @@ private long getOffset(final int levelOne, final int levelTwo) {
 		return p;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long findCRC32(AnyObjectId objId) throws MissingObjectException {
 		final int levelOne = objId.getFirstByte();
@@ -236,16 +242,19 @@ public long findCRC32(AnyObjectId objId) throws MissingObjectException {
 		return NB.decodeUInt32(crc32[levelOne], levelTwo << 2);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean hasCRC32Support() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<MutableEntry> iterator() {
 		return new EntriesIteratorV2();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void resolve(Set<ObjectId> matches, AbbreviatedObjectId id,
 			int matchLimit) throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriter.java
index 51539112e..b92f7b207 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriter.java
@@ -53,16 +53,16 @@
 
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.transport.PackedObjectInfo;
 import org.eclipse.jgit.util.NB;
 
 /**
- * Creates a table of contents to support random access by {@link PackFile}.
+ * Creates a table of contents to support random access by
+ * {@link org.eclipse.jgit.internal.storage.file.PackFile}.
  * <p>
- * Pack index files (the <code>.idx</code> suffix in a pack file pair)
- * provides random access to any object in the pack by associating an ObjectId
- * to the byte offset within the pack where the object's data can be read.
+ * Pack index files (the <code>.idx</code> suffix in a pack file pair) provides
+ * random access to any object in the pack by associating an ObjectId to the
+ * byte offset within the pack where the object's data can be read.
  */
 public abstract class PackIndexWriter {
 	/** Magic constant indicating post-version 1 format. */
@@ -90,7 +90,7 @@ public abstract class PackIndexWriter {
 	 *            will be examined until a format can be conclusively selected.
 	 * @return a new writer to output an index file of the requested format to
 	 *         the supplied stream.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             no recognized pack index version can support the supplied
 	 *             objects. This is likely a bug in the implementation.
 	 * @see #oldestPossibleFormat(List)
@@ -117,7 +117,7 @@ public static PackIndexWriter createOldestPossible(final OutputStream dst,
 	 *            the objects the caller needs to store in the index. Entries
 	 *            will be examined until a format can be conclusively selected.
 	 * @return the index format.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             no recognized pack index version can support the supplied
 	 *             objects. This is likely a bug in the implementation.
 	 */
@@ -143,7 +143,7 @@ public static int oldestPossibleFormat(
 	 *            this formatted version will be written.
 	 * @return a new writer to output an index file of the requested format to
 	 *         the supplied stream.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the version requested is not supported by this
 	 *             implementation.
 	 */
@@ -195,12 +195,13 @@ protected PackIndexWriter(final OutputStream dst) {
 	 *
 	 * @param toStore
 	 *            sorted list of objects to store in the index. The caller must
-	 *            have previously sorted the list using {@link PackedObjectInfo}'s
-	 *            native {@link Comparable} implementation.
+	 *            have previously sorted the list using
+	 *            {@link org.eclipse.jgit.transport.PackedObjectInfo}'s native
+	 *            {@link java.lang.Comparable} implementation.
 	 * @param packDataChecksum
 	 *            checksum signature of the entire pack data content. This is
 	 *            traditionally the last 20 bytes of the pack file's own stream.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream, or this
 	 *             index format cannot store the object data supplied.
 	 */
@@ -230,7 +231,7 @@ public void write(final List<? extends PackedObjectInfo> toStore,
 	 * the {@link #entries} collection may be iterated over more than once if
 	 * necessary. Implementors therefore have complete control over the data.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream, or this
 	 *             index format cannot store the object data supplied.
 	 */
@@ -246,7 +247,7 @@ public void write(final List<? extends PackedObjectInfo> toStore,
 	 *
 	 * @param version
 	 *            version number of this index format being written.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream.
 	 */
 	protected void writeTOC(final int version) throws IOException {
@@ -260,10 +261,10 @@ protected void writeTOC(final int version) throws IOException {
 	 * <p>
 	 * The fan-out table is 4 KB in size, holding 256 32-bit unsigned integer
 	 * counts. Each count represents the number of objects within this index
-	 * whose {@link ObjectId#getFirstByte()} matches the count's position in the
-	 * fan-out table.
+	 * whose {@link org.eclipse.jgit.lib.ObjectId#getFirstByte()} matches the
+	 * count's position in the fan-out table.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream.
 	 */
 	protected void writeFanOutTable() throws IOException {
@@ -288,7 +289,7 @@ protected void writeFanOutTable() throws IOException {
 	 * the pack data checksum above.</li>
 	 * </ol>
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred while writing to the output stream.
 	 */
 	protected void writeChecksumFooter() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV1.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV1.java
index 6017b997e..f220e7a6c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV1.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV1.java
@@ -68,6 +68,7 @@ static boolean canStore(final PackedObjectInfo oe) {
 		super(dst);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void writeImpl() throws IOException {
 		writeFanOutTable();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV2.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV2.java
index 770549d69..a18ccaf9e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV2.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackIndexWriterV2.java
@@ -63,6 +63,7 @@ class PackIndexWriterV2 extends PackIndexWriter {
 		super(dst);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void writeImpl() throws IOException {
 		writeTOC(2);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
index 962f765aa..8a4104aea 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
@@ -64,6 +64,7 @@ class PackInputStream extends InputStream {
 		wc.pin(pack, pos);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] b, int off, int len) throws IOException {
 		int n = wc.copy(pack, pos, b, off, len);
@@ -71,6 +72,7 @@ public int read(byte[] b, int off, int len) throws IOException {
 		return n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		byte[] buf = new byte[1];
@@ -78,6 +80,7 @@ public int read() throws IOException {
 		return n == 1 ? buf[0] & 0xff : -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		wc.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java
index 8c3bb0874..4643158c7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java
@@ -119,15 +119,20 @@ class PackInserter extends ObjectInserter {
 	}
 
 	/**
+	 * Whether to check if objects exist in the repo
+	 *
 	 * @param check
-	 *            if false, will write out possibly-duplicate objects without
-	 *            first checking whether they exist in the repo; default is true.
+	 *            if {@code false}, will write out possibly-duplicate objects
+	 *            without first checking whether they exist in the repo; default
+	 *            is true.
 	 */
 	public void checkExisting(boolean check) {
 		checkExisting = check;
 	}
 
 	/**
+	 * Set compression level for zlib deflater.
+	 *
 	 * @param compression
 	 *            compression level for zlib deflater.
 	 */
@@ -139,6 +144,7 @@ int getBufferSize() {
 		return buffer().length;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId insert(int type, byte[] data, int off, int len)
 			throws IOException {
@@ -157,6 +163,7 @@ public ObjectId insert(int type, byte[] data, int off, int len)
 		return endObject(id, offset);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId insert(int type, long len, InputStream in)
 			throws IOException {
@@ -230,16 +237,19 @@ private static int writePackHeader(byte[] buf, int objectCount) {
 		return 12;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PackParser newPackParser(InputStream in) {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectReader newReader() {
 		return new Reader();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		if (tmpPack == null) {
@@ -309,6 +319,7 @@ private ObjectId computeName(List<PackedObjectInfo> list) {
 		return ObjectId.fromRaw(md.digest());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackLock.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackLock.java
index a433dec54..82f0da1c8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackLock.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackLock.java
@@ -50,7 +50,10 @@
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 
-/** Keeps track of a {@link PackFile}'s associated <code>.keep</code> file. */
+/**
+ * Keeps track of a {@link org.eclipse.jgit.internal.storage.file.PackFile}'s
+ * associated <code>.keep</code> file.
+ */
 public class PackLock {
 	private final File keepFile;
 
@@ -74,7 +77,7 @@ public PackLock(final File packFile, final FS fs) {
 	 * @param msg
 	 *            message to store in the file.
 	 * @return true if the keep file was successfully written; false otherwise.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the keep file could not be written.
 	 */
 	public boolean lock(String msg) throws IOException {
@@ -92,7 +95,7 @@ public boolean lock(String msg) throws IOException {
 	/**
 	 * Remove the <code>.keep</code> file that holds this pack in place.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if deletion of .keep file failed
 	 */
 	public void unlock() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackReverseIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackReverseIndex.java
index fe9f70092..944af26dc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackReverseIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackReverseIndex.java
@@ -174,7 +174,7 @@ public ObjectId findObject(final long offset) {
 	 *            offset).
 	 * @return offset of the next object in a pack or maxOffset if provided
 	 *         offset was the last one.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             when there is no object with the provided offset.
 	 */
 	public long findNextOffset(final long offset, final long maxOffset)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
index a69f51928..200c63c17 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
@@ -125,6 +125,7 @@ class PackedBatchRefUpdate extends BatchRefUpdate {
 		this.refdb = refdb;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void execute(RevWalk walk, ProgressMonitor monitor,
 			List<String> options) throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index bd39e6565..8b3b79412 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -111,14 +111,14 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Traditional file system based {@link RefDatabase}.
+ * Traditional file system based {@link org.eclipse.jgit.lib.RefDatabase}.
  * <p>
  * This is the classical reference database representation for a Git repository.
  * References are stored in two formats: loose, and packed.
  * <p>
  * Loose references are stored as individual files within the {@code refs/}
  * directory. The file name matches the reference name and the file contents is
- * the current {@link ObjectId} in string form.
+ * the current {@link org.eclipse.jgit.lib.ObjectId} in string form.
  * <p>
  * Packed references are stored in a single text file named {@code packed-refs}.
  * In the packed format, each reference is stored on its own line. This file
@@ -243,6 +243,7 @@ public File logFor(String name) {
 		return new File(logsDir, name);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void create() throws IOException {
 		FileUtils.mkdir(refsDir);
@@ -251,6 +252,7 @@ public void create() throws IOException {
 		newLogWriter(false).create();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		clearReferences();
@@ -261,12 +263,14 @@ private void clearReferences() {
 		packedRefs.set(NO_PACKED_REFS);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void refresh() {
 		super.refresh();
 		clearReferences();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isNameConflicting(String name) throws IOException {
 		RefList<Ref> packed = getPackedRefs();
@@ -312,6 +316,7 @@ private RefList<LooseRef> getLooseRefs() {
 		return loose;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref exactRef(String name) throws IOException {
 		RefList<Ref> packed = getPackedRefs();
@@ -336,6 +341,7 @@ public Ref exactRef(String name) throws IOException {
 		return ref;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref getRef(final String needle) throws IOException {
 		final RefList<Ref> packed = getPackedRefs();
@@ -360,6 +366,7 @@ public Ref getRef(final String needle) throws IOException {
 		return ref;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<String, Ref> getRefs(String prefix) throws IOException {
 		final RefList<LooseRef> oldLoose = looseRefs.get();
@@ -399,6 +406,7 @@ public Map<String, Ref> getRefs(String prefix) throws IOException {
 		return new RefMap(prefix, packed, upcast(loose), symbolic.toRefList());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public List<Ref> getAdditionalRefs() throws IOException {
 		List<Ref> ret = new LinkedList<>();
@@ -533,6 +541,7 @@ private void scanOne(String name) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref peel(final Ref ref) throws IOException {
 		final Ref leaf = ref.getLeaf();
@@ -584,6 +593,7 @@ void storedSymbolicRef(RefDirectoryUpdate u, FileSnapshot snapshot,
 		fireRefsChanged();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public RefDirectoryUpdate newUpdate(String name, boolean detach)
 			throws IOException {
@@ -603,6 +613,7 @@ public RefDirectoryUpdate newUpdate(String name, boolean detach)
 		return refDirUpdate;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public RefDirectoryRename newRename(String fromName, String toName)
 			throws IOException {
@@ -611,11 +622,13 @@ public RefDirectoryRename newRename(String fromName, String toName)
 		return new RefDirectoryRename(from, to);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PackedBatchRefUpdate newBatchUpdate() {
 		return new PackedBatchRefUpdate(this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean performsAtomicTransactions() {
 		return true;
@@ -695,7 +708,7 @@ void delete(RefDirectoryUpdate update) throws IOException {
 	 *
 	 * @param refs
 	 *            the refs to be added. Must be fully qualified.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void pack(List<String> refs) throws IOException {
 		pack(refs, Collections.emptyMap());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
index 09456c85c..202e51f6c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
@@ -95,6 +95,7 @@ class RefDirectoryRename extends RefRename {
 		refdb = src.getRefDatabase();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected Result doRename() throws IOException {
 		if (source.getRef().isSymbolic())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
index 7ab30faf1..4d6b24570 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
@@ -65,16 +65,19 @@ class RefDirectoryUpdate extends RefUpdate {
 		database = r;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected RefDirectory getRefDatabase() {
 		return database;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected Repository getRepository() {
 		return database.getRepository();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean tryLock(boolean deref) throws IOException {
 		shouldDeref = deref;
@@ -92,6 +95,7 @@ protected boolean tryLock(boolean deref) throws IOException {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void unlock() {
 		if (lock != null) {
@@ -100,6 +104,7 @@ protected void unlock() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected Result doUpdate(final Result status) throws IOException {
 		WriteConfig wc = database.getRepository().getConfig()
@@ -141,6 +146,7 @@ private String toResultString(Result status) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected Result doDelete(final Result status) throws IOException {
 		if (getRef().getStorage() != Ref.Storage.NEW)
@@ -148,6 +154,7 @@ protected Result doDelete(final Result status) throws IOException {
 		return status;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected Result doLink(final String target) throws IOException {
 		WriteConfig wc = database.getRepository().getConfig()
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
index 8723a8b38..08a14b28d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
@@ -93,6 +93,7 @@ public class ReflogEntryImpl implements Serializable, ReflogEntry {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogEntry#getOldId()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getOldId() {
 		return oldId;
@@ -101,6 +102,7 @@ public ObjectId getOldId() {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogEntry#getNewId()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId getNewId() {
 		return newId;
@@ -109,6 +111,7 @@ public ObjectId getNewId() {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogEntry#getWho()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public PersonIdent getWho() {
 		return who;
@@ -117,11 +120,13 @@ public PersonIdent getWho() {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogEntry#getComment()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public String getComment() {
 		return comment;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
@@ -132,6 +137,7 @@ public String toString() {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogEntry#parseCheckout()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public CheckoutEntry parseCheckout() {
 		if (getComment().startsWith(CheckoutEntryImpl.CHECKOUT_MOVING_FROM))
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogReaderImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogReaderImpl.java
index c3702feca..e95e1c203 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogReaderImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogReaderImpl.java
@@ -74,6 +74,7 @@ class ReflogReaderImpl implements ReflogReader {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogReaader#getLastEntry()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public ReflogEntry getLastEntry() throws IOException {
 		return getReverseEntry(0);
@@ -82,6 +83,7 @@ public ReflogEntry getLastEntry() throws IOException {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogReaader#getReverseEntries()
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<ReflogEntry> getReverseEntries() throws IOException {
 		return getReverseEntries(Integer.MAX_VALUE);
@@ -90,6 +92,7 @@ public List<ReflogEntry> getReverseEntries() throws IOException {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogReaader#getReverseEntry(int)
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public ReflogEntry getReverseEntry(int number) throws IOException {
 		if (number < 0)
@@ -119,6 +122,7 @@ public ReflogEntry getReverseEntry(int number) throws IOException {
 	/* (non-Javadoc)
 	 * @see org.eclipse.jgit.internal.storage.file.ReflogReaader#getReverseEntries(int)
 	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<ReflogEntry> getReverseEntries(int max) throws IOException {
 		final byte[] log;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
index d1bd92220..d99c26614 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
@@ -95,6 +95,8 @@ public static String refLockFor(String name) {
 	 * Create writer for ref directory.
 	 *
 	 * @param refdb
+	 *            a {@link org.eclipse.jgit.internal.storage.file.RefDirectory}
+	 *            object.
 	 */
 	public ReflogWriter(RefDirectory refdb) {
 		this(refdb, false);
@@ -104,6 +106,8 @@ public ReflogWriter(RefDirectory refdb) {
 	 * Create writer for ref directory.
 	 *
 	 * @param refdb
+	 *            a {@link org.eclipse.jgit.internal.storage.file.RefDirectory}
+	 *            object.
 	 * @param forceWrite
 	 *            true to write to disk all entries logged, false to respect the
 	 *            repository's config and current log file status.
@@ -116,7 +120,7 @@ public ReflogWriter(RefDirectory refdb, boolean forceWrite) {
 	/**
 	 * Create the log directories.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @return this writer.
 	 */
 	public ReflogWriter create() throws IOException {
@@ -131,9 +135,11 @@ public ReflogWriter create() throws IOException {
 	 * Write the given entry to the ref's log.
 	 *
 	 * @param refName
+	 *            a {@link java.lang.String} object.
 	 * @param entry
+	 *            a {@link org.eclipse.jgit.lib.ReflogEntry} object.
 	 * @return this writer
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public ReflogWriter log(String refName, ReflogEntry entry)
 			throws IOException {
@@ -145,12 +151,17 @@ public ReflogWriter log(String refName, ReflogEntry entry)
 	 * Write the given entry information to the ref's log
 	 *
 	 * @param refName
+	 *            ref name
 	 * @param oldId
+	 *            old object id
 	 * @param newId
+	 *            new object id
 	 * @param ident
+	 *            a {@link org.eclipse.jgit.lib.PersonIdent}
 	 * @param message
+	 *            reflog message
 	 * @return this writer
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public ReflogWriter log(String refName, ObjectId oldId,
 			ObjectId newId, PersonIdent ident, String message) throws IOException {
@@ -162,10 +173,13 @@ public ReflogWriter log(String refName, ObjectId oldId,
 	 * Write the given ref update to the ref's log.
 	 *
 	 * @param update
+	 *            a {@link org.eclipse.jgit.lib.RefUpdate}
 	 * @param msg
+	 *            reflog message
 	 * @param deref
+	 *            whether to dereference symbolic refs
 	 * @return this writer
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public ReflogWriter log(RefUpdate update, String msg,
 			boolean deref) throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataInput.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataInput.java
index 452636dca..3b815b5c1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataInput.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataInput.java
@@ -64,83 +64,105 @@ class SimpleDataInput implements DataInput {
 		this.fd = fd;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int readInt() throws IOException {
 		readFully(buf, 0, 4);
 		return NB.decodeInt32(buf, 0);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long readLong() throws IOException {
 		readFully(buf, 0, 8);
 		return NB.decodeInt64(buf, 0);
 	}
 
+	/**
+	 * Read unsigned int
+	 *
+	 * @return a long.
+	 * @throws java.io.IOException
+	 *             if any.
+	 */
 	public long readUnsignedInt() throws IOException {
 		readFully(buf, 0, 4);
 		return NB.decodeUInt32(buf, 0);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void readFully(byte[] b) throws IOException {
 		readFully(b, 0, b.length);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void readFully(byte[] b, int off, int len) throws IOException {
 		IO.readFully(fd, b, off, len);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int skipBytes(int n) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean readBoolean() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public byte readByte() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int readUnsignedByte() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public short readShort() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int readUnsignedShort() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public char readChar() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public float readFloat() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public double readDouble() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String readLine() throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String readUTF() throws IOException {
 		throw new UnsupportedOperationException();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
index 5fe042924..7825b841e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
@@ -64,74 +64,88 @@ class SimpleDataOutput implements DataOutput {
 		this.fd = fd;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeShort(int v) throws IOException {
 		NB.encodeInt16(buf, 0, v);
 		fd.write(buf, 0, 2);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeInt(int v) throws IOException {
 		NB.encodeInt32(buf, 0, v);
 		fd.write(buf, 0, 4);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeLong(long v) throws IOException {
 		NB.encodeInt64(buf, 0, v);
 		fd.write(buf, 0, 8);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b, int off, int len) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeBoolean(boolean v) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeByte(int v) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeChar(int v) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeFloat(float v) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeDouble(double v) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeBytes(String s) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeChars(String s) throws IOException {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeUTF(String s) throws IOException {
 		throw new UnsupportedOperationException();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
index a02743720..adb05e4d9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObject.java
@@ -86,7 +86,7 @@ public class UnpackedObject {
 	 *            expected ObjectId of the object, used only for error reporting
 	 *            in exceptions.
 	 * @return loader to read the inflated contents.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be parsed.
 	 */
 	public static ObjectLoader parse(byte[] raw, AnyObjectId id)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
index 61960068b..213cacab8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
@@ -57,7 +57,8 @@
 import org.eclipse.jgit.storage.file.WindowCacheConfig;
 
 /**
- * Caches slices of a {@link PackFile} in memory for faster read access.
+ * Caches slices of a {@link org.eclipse.jgit.internal.storage.file.PackFile} in
+ * memory for faster read access.
  * <p>
  * The WindowCache serves as a Java based "buffer cache", loading segments of a
  * PackFile into the JVM heap prior to use. As JGit often wants to do reads of
@@ -111,8 +112,9 @@
  * {@link #createRef(PackFile, long, ByteWindow)} methods, and matching
  * decrements during {@link #clear(Ref)}. Implementors may need to override
  * {@link #createRef(PackFile, long, ByteWindow)} in order to embed additional
- * accounting information into an implementation specific {@link Ref} subclass,
- * as the cached entity may have already been evicted by the JRE's garbage
+ * accounting information into an implementation specific
+ * {@link org.eclipse.jgit.internal.storage.file.WindowCache.Ref} subclass, as
+ * the cached entity may have already been evicted by the JRE's garbage
  * collector.
  * <p>
  * To maintain higher concurrency workloads, during eviction only one thread
@@ -150,7 +152,7 @@ private static final int bits(int newSize) {
 	 * @deprecated use {@code cfg.install()} to avoid internal reference.
 	 * @param cfg
 	 *            the new window cache configuration.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the cache configuration contains one or more invalid
 	 *             settings, usually too low of a limit.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCursor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCursor.java
index 83b236ed9..569bfe895 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCursor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCursor.java
@@ -110,11 +110,13 @@ DeltaBaseCache getDeltaBaseCache() {
 		return baseCache;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectReader newReader() {
 		return new WindowCursor(db);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public BitmapIndex getBitmapIndex() throws IOException {
 		for (PackFile pack : db.getPacks()) {
@@ -125,6 +127,7 @@ public BitmapIndex getBitmapIndex() throws IOException {
 		return null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<CachedPack> getCachedPacksAndUpdate(
 			BitmapBuilder needBitmap) throws IOException {
@@ -137,6 +140,7 @@ public Collection<CachedPack> getCachedPacksAndUpdate(
 		return Collections.emptyList();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<ObjectId> resolve(AbbreviatedObjectId id)
 			throws IOException {
@@ -147,11 +151,13 @@ public Collection<ObjectId> resolve(AbbreviatedObjectId id)
 		return matches;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean has(AnyObjectId objectId) throws IOException {
 		return db.has(objectId);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectLoader open(AnyObjectId objectId, int typeHint)
 			throws MissingObjectException, IncorrectObjectTypeException,
@@ -168,11 +174,13 @@ public ObjectLoader open(AnyObjectId objectId, int typeHint)
 		return ldr;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Set<ObjectId> getShallowCommits() throws IOException {
 		return db.getShallowCommits();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getObjectSize(AnyObjectId objectId, int typeHint)
 			throws MissingObjectException, IncorrectObjectTypeException,
@@ -187,11 +195,13 @@ public long getObjectSize(AnyObjectId objectId, int typeHint)
 		return sz;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public LocalObjectToPack newObjectToPack(AnyObjectId objectId, int type) {
 		return new LocalObjectToPack(objectId, type);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void selectObjectRepresentation(PackWriter packer,
 			ProgressMonitor monitor, Iterable<ObjectToPack> objects)
@@ -202,6 +212,7 @@ public void selectObjectRepresentation(PackWriter packer,
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void copyObjectAsIs(PackOutputStream out, ObjectToPack otp,
 			boolean validate) throws IOException,
@@ -210,6 +221,7 @@ public void copyObjectAsIs(PackOutputStream out, ObjectToPack otp,
 		src.pack.copyAsIs(out, src, validate, this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void writeObjects(PackOutputStream out, List<ObjectToPack> list)
 			throws IOException {
@@ -253,6 +265,7 @@ int copy(final PackFile pack, long position, final byte[] dstbuf,
 		return cnt - need;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void copyPackAsIs(PackOutputStream out, CachedPack pack)
 			throws IOException {
@@ -348,13 +361,18 @@ void pin(final PackFile pack, final long position)
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@Nullable
 	public ObjectInserter getCreatedFromInserter() {
 		return createdFromInserter;
 	}
 
-	/** Release the current window cursor. */
+	/**
+	 * {@inheritDoc}
+	 * <p>
+	 * Release the current window cursor.
+	 */
 	@Override
 	public void close() {
 		window = null;