Fix javadoc in org.eclipse.jgit util packages

Change-Id: Ia655f45153bcf1d422ffffce6dcf914847e14c4c
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit/src/org/eclipse/jgit/util/Base64.java

@@ -19,14 +19,13 @@ import org.eclipse.jgit.internal.JGitText;
  * <p>
  * I am placing this code in the Public Domain. Do with it as you will. This
  * software comes with no guarantees or warranties but with plenty of
- * well-wishing instead! Please visit <a
- * href="http://iharder.net/base64">http://iharder.net/base64</a> periodically
- * to check for updates or to contribute improvements.
+ * well-wishing instead! Please visit
+ * <a href="http://iharder.net/base64">http://iharder.net/base64</a>
+ * periodically to check for updates or to contribute improvements.
  * </p>
  *
  * @author Robert Harder
  * @author rob@iharder.net
- * @version 2.1, stripped to minimum feature set used by JGit.
  */
 public class Base64 {
 	/** The equals sign (=) as a byte. */
@@ -248,7 +247,7 @@ public class Base64 {
 	 * @param len
 	 *            The length of characters to decode
 	 * @return decoded data
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the input is not a valid Base64 sequence.
 	 */
 	public static byte[] decode(byte[] source, int off, int len) {

org.eclipse.jgit/src/org/eclipse/jgit/util/BlockList.java

@@ -84,7 +84,9 @@ public class BlockList<T> extends AbstractList<T> {
 
 	private T[] tailBlock;
 
-	/** Initialize an empty list. */
+	/**
+	 * Initialize an empty list.
+	 */
 	public BlockList() {
 		directory = BlockList.<T> newDirectory(256);
 		directory[0] = BlockList.<T> newBlock();
@@ -106,11 +108,13 @@ public class BlockList<T> extends AbstractList<T> {
 		tailBlock = directory[0];
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int size() {
 		return size;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void clear() {
 		for (T[] block : directory) {
@@ -123,6 +127,7 @@ public class BlockList<T> extends AbstractList<T> {
 		tailBlock = directory[0];
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public T get(int index) {
 		if (index < 0 || size <= index)
@@ -130,6 +135,7 @@ public class BlockList<T> extends AbstractList<T> {
 		return directory[toDirectoryIndex(index)][toBlockIndex(index)];
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public T set(int index, T element) {
 		if (index < 0 || size <= index)
@@ -187,6 +193,7 @@ public class BlockList<T> extends AbstractList<T> {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean add(T element) {
 		int i = tailBlkIdx;
@@ -217,6 +224,7 @@ public class BlockList<T> extends AbstractList<T> {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void add(int index, T element) {
 		if (index == size) {
@@ -238,6 +246,7 @@ public class BlockList<T> extends AbstractList<T> {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public T remove(int index) {
 		if (index == size - 1) {
@@ -277,6 +286,7 @@ public class BlockList<T> extends AbstractList<T> {
 		tailBlock = directory[tailDirIdx];
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<T> iterator() {
 		return new MyIterator();

org.eclipse.jgit/src/org/eclipse/jgit/util/CachedAuthenticator.java

@@ -49,7 +49,9 @@ import java.net.PasswordAuthentication;
 import java.util.Collection;
 import java.util.concurrent.CopyOnWriteArrayList;
 
-/** Abstract authenticator which remembers prior authentications. */
+/**
+ * Abstract authenticator which remembers prior authentications.
+ */
 public abstract class CachedAuthenticator extends Authenticator {
 	private static final Collection<CachedAuthentication> cached = new CopyOnWriteArrayList<>();
 
@@ -63,6 +65,7 @@ public abstract class CachedAuthenticator extends Authenticator {
 		cached.add(ca);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected final PasswordAuthentication getPasswordAuthentication() {
 		final String host = getRequestingHost();

org.eclipse.jgit/src/org/eclipse/jgit/util/ChangeIdUtil.java

@@ -82,9 +82,11 @@ public class ChangeIdUtil {
 	 * @param firstParentId
 	 *            parent id of previous commit or null
 	 * @param author
-	 *            the {@link PersonIdent} for the presumed author and time
+	 *            the {@link org.eclipse.jgit.lib.PersonIdent} for the presumed
+	 *            author and time
 	 * @param committer
-	 *            the {@link PersonIdent} for the presumed committer and time
+	 *            the {@link org.eclipse.jgit.lib.PersonIdent} for the presumed
+	 *            committer and time
 	 * @param message
 	 *            The commit message
 	 * @return the change id SHA1 string (without the 'I') or null if the
@@ -138,7 +140,9 @@ public class ChangeIdUtil {
 	 * line.
 	 *
 	 * @param message
+	 *            a message.
 	 * @param changeId
+	 *            a Change-Id.
 	 * @return a commit message with an inserted Change-Id line
 	 */
 	public static String insertId(String message, ObjectId changeId) {
@@ -148,18 +152,21 @@ public class ChangeIdUtil {
 	/**
 	 * Find the right place to insert a Change-Id and return it.
 	 * <p>
-	 * If no Change-Id is found the Change-Id is inserted before
-	 * the first footer line but after a Bug line.
+	 * If no Change-Id is found the Change-Id is inserted before the first
+	 * footer line but after a Bug line.
 	 *
-	 * If Change-Id is found and replaceExisting is set to false,
-	 * the message is unchanged.
+	 * If Change-Id is found and replaceExisting is set to false, the message is
+	 * unchanged.
 	 *
-	 * If Change-Id is found and replaceExisting is set to true,
-	 * the Change-Id is replaced with {@code changeId}.
+	 * If Change-Id is found and replaceExisting is set to true, the Change-Id
+	 * is replaced with {@code changeId}.
 	 *
 	 * @param message
+	 *            a message.
 	 * @param changeId
+	 *            a Change-Id.
 	 * @param replaceExisting
+	 *            a boolean.
 	 * @return a commit message with an inserted Change-Id line
 	 */
 	public static String insertId(String message, ObjectId changeId,
@@ -219,6 +226,7 @@ public class ChangeIdUtil {
 	 * only lines matching {@code footerPattern}.
 	 *
 	 * @param message
+	 *            a message.
 	 * @param delimiter
 	 *            the line delimiter, like "\n" or "\r\n", needed to find the
 	 *            footer

org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java

@@ -75,7 +75,9 @@ import org.eclipse.jgit.util.ProcessResult.Status;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-/** Abstraction to support various file system operations not in Java. */
+/**
+ * Abstraction to support various file system operations not in Java.
+ */
 public abstract class FS {
 	private static final Logger LOG = LoggerFactory.getLogger(FS.class);
 
@@ -192,7 +194,6 @@ public abstract class FS {
 	 *            </ul>
 	 *
 	 *            Note: this parameter is only relevant on Windows.
-	 *
 	 * @return detected file system abstraction
 	 */
 	public static FS detect(Boolean cygwinUsed) {
@@ -224,7 +225,11 @@ public abstract class FS {
 		gitSystemConfig = src.gitSystemConfig;
 	}
 
-	/** @return a new instance of the same type of FS. */
+	/**
+	 * Create a new instance of the same type of FS.
+	 *
+	 * @return a new instance of the same type of FS.
+	 */
 	public abstract FS newInstance();
 
 	/**
@@ -242,8 +247,8 @@ public abstract class FS {
 	 * parallel only one will succeed. In such cases both clients may think they
 	 * created a new file.
 	 *
-	 * @return true if this implementation support atomic creation of new
-	 *         Files by {@link File#createNewFile()}
+	 * @return true if this implementation support atomic creation of new Files
+	 *         by {@link java.io.File#createNewFile()}
 	 * @since 4.5
 	 */
 	public boolean supportsAtomicCreateNewFile() {
@@ -305,8 +310,9 @@ public abstract class FS {
 	 * than that of the link target.
 	 *
 	 * @param f
+	 *            a {@link java.io.File} object.
 	 * @return last modified time of f
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public long lastModified(File f) throws IOException {
@@ -318,8 +324,10 @@ public abstract class FS {
 	 * symbolic links, the link is modified, not the target,
 	 *
 	 * @param f
+	 *            a {@link java.io.File} object.
 	 * @param time
-	 * @throws IOException
+	 *            last modified time
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void setLastModified(File f, long time) throws IOException {
@@ -331,8 +339,9 @@ public abstract class FS {
 	 * it's the length of the link, else the length of the target.
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return length of a file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public long length(File path) throws IOException {
@@ -343,7 +352,8 @@ public abstract class FS {
 	 * Delete a file. Throws an exception if delete fails.
 	 *
 	 * @param f
-	 * @throws IOException
+	 *            a {@link java.io.File} object.
+	 * @throws java.io.IOException
 	 *             this may be a Java7 subclass with detailed information
 	 * @since 3.3
 	 */
@@ -444,7 +454,7 @@ public abstract class FS {
 	 *            Files to search for in the given path
 	 * @return the first match found, or null
 	 * @since 3.0
-	 **/
+	 */
 	protected static File searchPath(final String path, final String... lookFor) {
 		if (path == null)
 			return null;
@@ -470,7 +480,7 @@ public abstract class FS {
 	 *            to be used to parse the command's output
 	 * @return the one-line output of the command or {@code null} if there is
 	 *         none
-	 * @throws CommandFailedException
+	 * @throws org.eclipse.jgit.errors.CommandFailedException
 	 *             thrown when the command failed (return code was non-zero)
 	 */
 	@Nullable
@@ -493,7 +503,7 @@ public abstract class FS {
 	 *            current process
 	 * @return the one-line output of the command or {@code null} if there is
 	 *         none
-	 * @throws CommandFailedException
+	 * @throws org.eclipse.jgit.errors.CommandFailedException
 	 *             thrown when the command failed (return code was non-zero)
 	 * @since 4.0
 	 */
@@ -632,6 +642,8 @@ public abstract class FS {
 	}
 
 	/**
+	 * Discover the path to the Git executable.
+	 *
 	 * @return the path to the Git executable or {@code null} if it cannot be
 	 *         determined.
 	 * @since 4.0
@@ -639,6 +651,8 @@ public abstract class FS {
 	protected abstract File discoverGitExe();
 
 	/**
+	 * Discover the path to the system-wide Git configuration file
+	 *
 	 * @return the path to the system-wide Git configuration file or
 	 *         {@code null} if it cannot be determined.
 	 * @since 4.0
@@ -686,8 +700,10 @@ public abstract class FS {
 	}
 
 	/**
-	 * @return the currently used path to the system-wide Git configuration
-	 *         file or {@code null} if none has been set.
+	 * Get the currently used path to the system-wide Git configuration file.
+	 *
+	 * @return the currently used path to the system-wide Git configuration file
+	 *         or {@code null} if none has been set.
 	 * @since 4.0
 	 */
 	public File getGitSystemConfig() {
@@ -711,7 +727,10 @@ public abstract class FS {
 	}
 
 	/**
+	 * Get the parent directory of this file's parent directory
+	 *
 	 * @param grandchild
+	 *            a {@link java.io.File} object.
 	 * @return the parent directory of this file's parent directory or
 	 *         {@code null} in case there's no grandparent directory
 	 * @since 4.0
@@ -729,8 +748,9 @@ public abstract class FS {
 	 * Check if a file is a symbolic link and read it
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return target of link or null
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public String readSymLink(File path) throws IOException {
@@ -738,9 +758,12 @@ public abstract class FS {
 	}
 
 	/**
+	 * Whether the path is a symbolic link (and we support these).
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return true if the path is a symbolic link (and we support these)
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public boolean isSymLink(File path) throws IOException {
@@ -752,6 +775,7 @@ public abstract class FS {
 	 * target does not exist
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return true if path exists
 	 * @since 3.0
 	 */
@@ -764,6 +788,7 @@ public abstract class FS {
 	 * path is a symbolic link to a directory, this method returns false.
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return true if file is a directory,
 	 * @since 3.0
 	 */
@@ -776,6 +801,7 @@ public abstract class FS {
 	 * symbolic links the test returns false if path represents a symbolic link.
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return true if path represents a regular file
 	 * @since 3.0
 	 */
@@ -784,10 +810,14 @@ public abstract class FS {
 	}
 
 	/**
+	 * Whether path is hidden, either starts with . on unix or has the hidden
+	 * attribute in windows
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return true if path is hidden, either starts with . on unix or has the
 	 *         hidden attribute in windows
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public boolean isHidden(File path) throws IOException {
@@ -798,8 +828,10 @@ public abstract class FS {
 	 * Set the hidden attribute for file whose name starts with a period.
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @param hidden
-	 * @throws IOException
+	 *            whether to set the file hidden
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void setHidden(File path, boolean hidden) throws IOException {
@@ -810,8 +842,10 @@ public abstract class FS {
 	 * Create a symbolic link
 	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @param target
-	 * @throws IOException
+	 *            target path of the symlink
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public void createSymLink(File path, String target) throws IOException {
@@ -819,15 +853,15 @@ public abstract class FS {
 	}
 
 	/**
-	 * Create a new file. See {@link File#createNewFile()}. Subclasses of this
-	 * class may take care to provide a safe implementation for this even if
-	 * {@link #supportsAtomicCreateNewFile()} is <code>false</code>
+	 * Create a new file. See {@link java.io.File#createNewFile()}. Subclasses
+	 * of this class may take care to provide a safe implementation for this
+	 * even if {@link #supportsAtomicCreateNewFile()} is <code>false</code>
 	 *
 	 * @param path
 	 *            the file to be created
 	 * @return <code>true</code> if the file was created, <code>false</code> if
 	 *         the file already existed
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.5
 	 */
 	public boolean createNewFile(File path) throws IOException {
@@ -835,7 +869,8 @@ public abstract class FS {
 	}
 
 	/**
-	 * See {@link FileUtils#relativizePath(String, String, String, boolean)}.
+	 * See
+	 * {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}.
 	 *
 	 * @param base
 	 *            The path against which <code>other</code> should be
@@ -868,7 +903,7 @@ public abstract class FS {
 	 *            Arguments to pass to this hook. Cannot be <code>null</code>,
 	 *            but can be an empty array.
 	 * @return The ProcessResult describing this hook's execution.
-	 * @throws JGitInternalException
+	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
@@ -903,7 +938,7 @@ public abstract class FS {
 	 *            A string to pass on to the standard input of the hook. May be
 	 *            <code>null</code>.
 	 * @return The ProcessResult describing this hook's execution.
-	 * @throws JGitInternalException
+	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
@@ -939,7 +974,7 @@ public abstract class FS {
 	 *            A string to pass on to the standard input of the hook. May be
 	 *            <code>null</code>.
 	 * @return The ProcessResult describing this hook's execution.
-	 * @throws JGitInternalException
+	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             if we fail to run the hook somehow. Causes may include an
 	 *             interrupted process or I/O errors.
 	 * @since 4.0
@@ -984,8 +1019,8 @@ public abstract class FS {
 	 *            The repository within which to find a hook.
 	 * @param hookName
 	 *            The name of the hook we're trying to find.
-	 * @return The {@link File} containing this particular hook if it exists in
-	 *         the given repository, <code>null</code> otherwise.
+	 * @return The {@link java.io.File} containing this particular hook if it
+	 *         exists in the given repository, <code>null</code> otherwise.
 	 * @since 4.0
 	 */
 	public File findHook(Repository repository, final String hookName) {
@@ -1015,9 +1050,9 @@ public abstract class FS {
 	 *            A string to pass on to the standard input of the hook. Can be
 	 *            <code>null</code>.
 	 * @return the exit value of this process.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if an I/O error occurs while executing this process.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             if the current thread is interrupted while waiting for the
 	 *             process to end.
 	 * @since 4.2
@@ -1051,9 +1086,9 @@ public abstract class FS {
 	 *            will be consumed by the process. The method will close the
 	 *            inputstream after all bytes are read.
 	 * @return the return code of this process.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if an I/O error occurs while executing this process.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             if the current thread is interrupted while waiting for the
 	 *             process to end.
 	 * @since 4.2
@@ -1179,15 +1214,15 @@ public abstract class FS {
 	public abstract ProcessBuilder runInShell(String cmd, String[] args);
 
 	/**
-	 * Execute a command defined by a {@link ProcessBuilder}.
+	 * Execute a command defined by a {@link java.lang.ProcessBuilder}.
 	 *
 	 * @param pb
 	 *            The command to be executed
 	 * @param in
 	 *            The standard input stream passed to the process
 	 * @return The result of the executed command
-	 * @throws InterruptedException
-	 * @throws IOException
+	 * @throws java.lang.InterruptedException
+	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	public ExecutionResult execute(ProcessBuilder pb, InputStream in)
@@ -1340,8 +1375,11 @@ public abstract class FS {
 	}
 
 	/**
+	 * Get the file attributes we care for.
+	 *
 	 * @param path
-	 * @return the file attributes we care for
+	 *            a {@link java.io.File} object.
+	 * @return the file attributes we care for.
 	 * @since 3.3
 	 */
 	public Attributes getAttributes(File path) {
@@ -1361,6 +1399,7 @@ public abstract class FS {
 	 * Normalize the unicode path to composed form.
 	 *
 	 * @param file
+	 *            a {@link java.io.File} object.
 	 * @return NFC-format File
 	 * @since 3.3
 	 */
@@ -1372,6 +1411,7 @@ public abstract class FS {
 	 * Normalize the unicode path to composed form.
 	 *
 	 * @param name
+	 *            path name
 	 * @return NFC-format string
 	 * @since 3.3
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java

@@ -86,7 +86,9 @@ public class FS_POSIX extends FS {
 		SUPPORTED, NOT_SUPPORTED, UNDEFINED
 	}
 
-	/** Default constructor. */
+	/**
+	 * Default constructor.
+	 */
 	protected FS_POSIX() {
 	}
 
@@ -134,6 +136,7 @@ public class FS_POSIX extends FS {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FS newInstance() {
 		return new FS_POSIX(this);
@@ -181,6 +184,7 @@ public class FS_POSIX extends FS {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected File discoverGitExe() {
 		String path = SystemReader.getInstance().getenv("PATH"); //$NON-NLS-1$
@@ -211,21 +215,25 @@ public class FS_POSIX extends FS {
 		return gitExe;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCaseSensitive() {
 		return !SystemReader.getInstance().isMacOS();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supportsExecute() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean canExecute(File f) {
 		return FileUtils.canExecute(f);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean setExecute(File f, boolean canExecute) {
 		if (!isFile(f))
@@ -266,6 +274,7 @@ public class FS_POSIX extends FS {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ProcessBuilder runInShell(String cmd, String[] args) {
 		List<String> argv = new ArrayList<>(4 + args.length);
@@ -279,9 +288,7 @@ public class FS_POSIX extends FS {
 		return proc;
 	}
 
-	/**
-	 * @since 4.0
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public ProcessResult runHookIfPresent(Repository repository, String hookName,
 			String[] args, PrintStream outRedirect, PrintStream errRedirect,
@@ -290,48 +297,43 @@ public class FS_POSIX extends FS {
 				errRedirect, stdinArgs);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean retryFailedLockFileCommit() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supportsSymlinks() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setHidden(File path, boolean hidden) throws IOException {
 		// no action on POSIX
 	}
 
-	/**
-	 * @since 3.3
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Attributes getAttributes(File path) {
 		return FileUtils.getFileAttributesPosix(this, path);
 	}
 
-	/**
-	 * @since 3.3
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public File normalize(File file) {
 		return FileUtils.normalize(file);
 	}
 
-	/**
-	 * @since 3.3
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public String normalize(String name) {
 		return FileUtils.normalize(name);
 	}
 
-	/**
-	 * @since 3.7
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public File findHook(Repository repository, String hookName) {
 		final File gitdir = repository.getDirectory();
@@ -345,6 +347,7 @@ public class FS_POSIX extends FS {
 		return null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supportsAtomicCreateNewFile() {
 		if (supportsAtomicCreateNewFile == AtomicFileCreation.UNDEFINED) {
@@ -356,13 +359,15 @@ public class FS_POSIX extends FS {
 	@Override
 	@SuppressWarnings("boxing")
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * An implementation of the File#createNewFile() semantics which works also
 	 * on NFS. If the config option
 	 * {@code core.supportsAtomicCreateNewFile = true} (which is the default)
 	 * then simply File#createNewFile() is called.
 	 *
 	 * But if {@code core.supportsAtomicCreateNewFile = false} then after
-	 * successful creation of the lock file a hardlink to that lock file is
+	 * successful creation of the lock file a hard link to that lock file is
 	 * created and the attribute nlink of the lock file is checked to be 2. If
 	 * multiple clients manage to create the same lock file nlink would be
 	 * greater than 2 showing the error.

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java

@@ -83,36 +83,43 @@ public class FS_Win32 extends FS {
 		super(src);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FS newInstance() {
 		return new FS_Win32(this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supportsExecute() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean canExecute(final File f) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean setExecute(final File f, final boolean canExec) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCaseSensitive() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean retryFailedLockFileCommit() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected File discoverGitExe() {
 		String path = SystemReader.getInstance().getenv("PATH"); //$NON-NLS-1$
@@ -141,6 +148,7 @@ public class FS_Win32 extends FS {
 		return gitExe;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected File userHomeImpl() {
 		String home = SystemReader.getInstance().getenv("HOME"); //$NON-NLS-1$
@@ -160,6 +168,7 @@ public class FS_Win32 extends FS {
 		return super.userHomeImpl();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ProcessBuilder runInShell(String cmd, String[] args) {
 		List<String> argv = new ArrayList<>(3 + args.length);
@@ -172,6 +181,7 @@ public class FS_Win32 extends FS {
 		return proc;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supportsSymlinks() {
 		if (supportSymlinks == null)
@@ -200,9 +210,7 @@ public class FS_Win32 extends FS {
 		}
 	}
 
-	/**
-	 * @since 3.3
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Attributes getAttributes(File path) {
 		return FileUtils.getFileAttributesBasic(this, path);

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32_Cygwin.java

@@ -72,6 +72,8 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 	private static String cygpath;
 
 	/**
+	 * Whether cygwin is found
+	 *
 	 * @return true if cygwin is found
 	 */
 	public static boolean isCygwin() {
@@ -107,11 +109,13 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 		super(src);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FS newInstance() {
 		return new FS_Win32_Cygwin(this);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public File resolve(final File dir, final String pn) {
 		String useCygPath = System.getProperty("jgit.usecygpath"); //$NON-NLS-1$
@@ -132,6 +136,7 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 		return super.resolve(dir, pn);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected File userHomeImpl() {
 		final String home = AccessController
@@ -146,6 +151,7 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 		return resolve(new File("."), home); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ProcessBuilder runInShell(String cmd, String[] args) {
 		List<String> argv = new ArrayList<>(4 + args.length);
@@ -159,18 +165,14 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 		return proc;
 	}
 
-	/**
-	 * @since 3.7
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public String relativize(String base, String other) {
 		final String relativized = super.relativize(base, other);
 		return relativized.replace(File.separatorChar, '/');
 	}
 
-	/**
-	 * @since 4.0
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public ProcessResult runHookIfPresent(Repository repository, String hookName,
 			String[] args, PrintStream outRedirect, PrintStream errRedirect,
@@ -179,9 +181,7 @@ public class FS_Win32_Cygwin extends FS_Win32 {
 				errRedirect, stdinArgs);
 	}
 
-	/**
-	 * @since 3.7
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public File findHook(Repository repository, String hookName) {
 		final File gitdir = repository.getDirectory();

org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtil.java

@@ -45,7 +45,6 @@ package org.eclipse.jgit.util;
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 
 import org.eclipse.jgit.util.FS.Attributes;
 
@@ -56,10 +55,14 @@ import org.eclipse.jgit.util.FS.Attributes;
 public class FileUtil {
 
 	/**
+	 * Read target path of a symlink.
+	 *
 	 * @param path
-	 * @return target path of the symlink
-	 * @throws IOException
-	 * @deprecated use {@link FileUtils#readSymLink(File)} instead
+	 *            a {@link java.io.File}.
+	 * @return target path of the symlink.
+	 * @throws java.io.IOException
+	 * @deprecated use {@link org.eclipse.jgit.util.FileUtils#readSymLink(File)}
+	 *             instead
 	 */
 	@Deprecated
 	public static String readSymlink(File path) throws IOException {
@@ -67,12 +70,16 @@ public class FileUtil {
 	}
 
 	/**
+	 * Create a symlink
+	 *
 	 * @param path
 	 *            path of the symlink to be created
 	 * @param target
 	 *            target of the symlink to be created
-	 * @throws IOException
-	 * @deprecated use {@link FileUtils#createSymLink(File, String)} instead
+	 * @throws java.io.IOException
+	 * @deprecated use
+	 *             {@link org.eclipse.jgit.util.FileUtils#createSymLink(File, String)}
+	 *             instead
 	 */
 	@Deprecated
 	public static void createSymLink(File path, String target)
@@ -81,9 +88,14 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether the passed file is a symlink
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return {@code true} if the passed path is a symlink
-	 * @deprecated Use {@link Files#isSymbolicLink(java.nio.file.Path)} instead
+	 * @deprecated Use
+	 *             {@link java.nio.file.Files#isSymbolicLink(java.nio.file.Path)}
+	 *             instead
 	 */
 	@Deprecated
 	public static boolean isSymlink(File path) {
@@ -91,11 +103,14 @@ public class FileUtil {
 	}
 
 	/**
+	 * Get lastModified attribute for given path
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @return lastModified attribute for given path
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @deprecated Use
-	 *             {@link Files#getLastModifiedTime(java.nio.file.Path, java.nio.file.LinkOption...)}
+	 *             {@link java.nio.file.Files#getLastModifiedTime(java.nio.file.Path, java.nio.file.LinkOption...)}
 	 *             instead
 	 */
 	@Deprecated
@@ -104,11 +119,15 @@ public class FileUtil {
 	}
 
 	/**
+	 * Set lastModified attribute for given path
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @param time
-	 * @throws IOException
+	 *            a long.
+	 * @throws java.io.IOException
 	 * @deprecated Use
-	 *             {@link Files#setLastModifiedTime(java.nio.file.Path, java.nio.file.attribute.FileTime)}
+	 *             {@link java.nio.file.Files#setLastModifiedTime(java.nio.file.Path, java.nio.file.attribute.FileTime)}
 	 *             instead
 	 */
 	@Deprecated
@@ -117,10 +136,13 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether this file exists
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @return {@code true} if the given path exists
 	 * @deprecated Use
-	 *             {@link Files#exists(java.nio.file.Path, java.nio.file.LinkOption...)}
+	 *             {@link java.nio.file.Files#exists(java.nio.file.Path, java.nio.file.LinkOption...)}
 	 *             instead
 	 */
 	@Deprecated
@@ -129,10 +151,14 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether this file is hidden
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @return {@code true} if the given path is hidden
-	 * @throws IOException
-	 * @deprecated Use {@link Files#isHidden(java.nio.file.Path)} instead
+	 * @throws java.io.IOException
+	 * @deprecated Use {@link java.nio.file.Files#isHidden(java.nio.file.Path)}
+	 *             instead
 	 */
 	@Deprecated
 	public static boolean isHidden(File path) throws IOException {
@@ -140,10 +166,16 @@ public class FileUtil {
 	}
 
 	/**
+	 * Set this file hidden
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @param hidden
-	 * @throws IOException
-	 * @deprecated Use {@link FileUtils#setHidden(File,boolean)} instead
+	 *            a boolean.
+	 * @throws java.io.IOException
+	 * @deprecated Use
+	 *             {@link org.eclipse.jgit.util.FileUtils#setHidden(File,boolean)}
+	 *             instead
 	 */
 	@Deprecated
 	public static void setHidden(File path, boolean hidden) throws IOException {
@@ -151,10 +183,14 @@ public class FileUtil {
 	}
 
 	/**
+	 * Get file length
+	 *
 	 * @param path
+	 *            a {@link java.io.File}.
 	 * @return length of the given file
-	 * @throws IOException
-	 * @deprecated Use {@link FileUtils#getLength(File)} instead
+	 * @throws java.io.IOException
+	 * @deprecated Use {@link org.eclipse.jgit.util.FileUtils#getLength(File)}
+	 *             instead
 	 */
 	@Deprecated
 	public static long getLength(File path) throws IOException {
@@ -162,10 +198,13 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether the given File is a directory
+	 *
 	 * @param path
-	 * @return {@code true} if the given file a directory
+	 *            a {@link java.io.File} object.
+	 * @return {@code true} if the given file is a directory
 	 * @deprecated Use
-	 *             {@link Files#isDirectory(java.nio.file.Path, java.nio.file.LinkOption...)}
+	 *             {@link java.nio.file.Files#isDirectory(java.nio.file.Path, java.nio.file.LinkOption...)}
 	 *             instead
 	 */
 	@Deprecated
@@ -174,10 +213,13 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether the given File is a file
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return {@code true} if the given file is a file
 	 * @deprecated Use
-	 *             {@link Files#isRegularFile(java.nio.file.Path, java.nio.file.LinkOption...)}
+	 *             {@link java.nio.file.Files#isRegularFile(java.nio.file.Path, java.nio.file.LinkOption...)}
 	 *             instead
 	 */
 	@Deprecated
@@ -186,9 +228,13 @@ public class FileUtil {
 	}
 
 	/**
+	 * Whether the given file can be executed
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return {@code true} if the given file can be executed
-	 * @deprecated Use {@link FileUtils#canExecute(File)} instead
+	 * @deprecated Use {@link org.eclipse.jgit.util.FileUtils#canExecute(File)}
+	 *             instead
 	 */
 	@Deprecated
 	public static boolean canExecute(File path) {
@@ -196,9 +242,12 @@ public class FileUtil {
 	}
 
 	/**
+	 * Delete the given file
+	 *
 	 * @param path
-	 * @throws IOException
-	 * @deprecated use {@link FileUtils#delete(File)}
+	 *            a {@link java.io.File} object.
+	 * @throws java.io.IOException
+	 * @deprecated use {@link org.eclipse.jgit.util.FileUtils#delete(File)}
 	 */
 	@Deprecated
 	public static void delete(File path) throws IOException {
@@ -206,10 +255,16 @@ public class FileUtil {
 	}
 
 	/**
+	 * Get file system attributes for the given file
+	 *
 	 * @param fs
+	 *            a {@link org.eclipse.jgit.util.FS} object.
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return file system attributes for the given file
-	 * @deprecated Use {@link FileUtils#getFileAttributesPosix(FS,File)} instead
+	 * @deprecated Use
+	 *             {@link org.eclipse.jgit.util.FileUtils#getFileAttributesPosix(FS,File)}
+	 *             instead
 	 */
 	@Deprecated
 	public static Attributes getFileAttributesPosix(FS fs, File path) {
@@ -217,9 +272,14 @@ public class FileUtil {
 	}
 
 	/**
+	 * NFC normalize File (on Mac), otherwise do nothing
+	 *
 	 * @param file
-	 * @return on Mac: NFC normalized {@link File}, otherwise the passed file
-	 * @deprecated Use {@link FileUtils#normalize(File)} instead
+	 *            a {@link java.io.File}.
+	 * @return on Mac: NFC normalized {@link java.io.File}, otherwise the passed
+	 *         file
+	 * @deprecated Use {@link org.eclipse.jgit.util.FileUtils#normalize(File)}
+	 *             instead
 	 */
 	@Deprecated
 	public static File normalize(File file) {
@@ -227,9 +287,13 @@ public class FileUtil {
 	}
 
 	/**
+	 * NFC normalize file name (on Mac), otherwise do nothing
+	 *
 	 * @param name
+	 *            a {@link java.lang.String} object.
 	 * @return on Mac: NFC normalized form of given name
-	 * @deprecated Use {@link FileUtils#normalize(String)} instead
+	 * @deprecated Use {@link org.eclipse.jgit.util.FileUtils#normalize(String)}
+	 *             instead
 	 */
 	@Deprecated
 	public static String normalize(String name) {

org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java

@@ -47,7 +47,6 @@ package org.eclipse.jgit.util;
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.channels.FileLock;
 import java.nio.file.AtomicMoveNotSupportedException;
 import java.nio.file.CopyOption;
 import java.nio.file.Files;
@@ -118,10 +117,9 @@ public class FileUtils {
 	 * @param f
 	 *            {@code File} to be converted to {@code Path}
 	 * @return the path represented by the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             in case the path represented by the file is not valid (
 	 *             {@link java.nio.file.InvalidPathException})
-	 *
 	 * @since 4.10
 	 */
 	public static Path toPath(final File f) throws IOException {
@@ -137,11 +135,11 @@ public class FileUtils {
 	 *
 	 * @param f
 	 *            {@code File} to be deleted
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if deletion of {@code f} fails. This may occur if {@code f}
 	 *             didn't exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to delete the same file.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to delete the same file.
 	 */
 	public static void delete(final File f) throws IOException {
 		delete(f, NONE);
@@ -157,12 +155,12 @@ public class FileUtils {
 	 *            a subtree, {@code RETRY} to retry when deletion failed.
 	 *            Retrying may help if the underlying file system doesn't allow
 	 *            deletion of files being read by another thread.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if deletion of {@code f} fails. This may occur if {@code f}
 	 *             didn't exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to delete the same file. This
-	 *             exception is not thrown when IGNORE_ERRORS is set.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to delete the same file.
+	 *             This exception is not thrown when IGNORE_ERRORS is set.
 	 */
 	public static void delete(final File f, int options) throws IOException {
 		FS fs = FS.DETECTED;
@@ -239,7 +237,7 @@ public class FileUtils {
 	 *            the old {@code File}
 	 * @param dst
 	 *            the new {@code File}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if the rename has failed
 	 * @since 3.0
 	 */
@@ -249,18 +247,20 @@ public class FileUtils {
 	}
 
 	/**
-	 * Rename a file or folder using the passed {@link CopyOption}s. If the
-	 * rename fails and if we are running on a filesystem where it makes sense
-	 * to repeat a failing rename then repeat the rename operation up to 9 times
-	 * with 100ms sleep time between two calls. Furthermore if the destination
-	 * exists and is a directory hierarchy with only directories in it, the
-	 * whole directory hierarchy will be deleted. If the target represents a
-	 * non-empty directory structure, empty subdirectories within that structure
-	 * may or may not be deleted even if the method fails. Furthermore if the
-	 * destination exists and is a file then the file will be replaced if
-	 * {@link StandardCopyOption#REPLACE_EXISTING} has been set. If
-	 * {@link StandardCopyOption#ATOMIC_MOVE} has been set the rename will be
-	 * done atomically or fail with an {@link AtomicMoveNotSupportedException}
+	 * Rename a file or folder using the passed
+	 * {@link java.nio.file.CopyOption}s. If the rename fails and if we are
+	 * running on a filesystem where it makes sense to repeat a failing rename
+	 * then repeat the rename operation up to 9 times with 100ms sleep time
+	 * between two calls. Furthermore if the destination exists and is a
+	 * directory hierarchy with only directories in it, the whole directory
+	 * hierarchy will be deleted. If the target represents a non-empty directory
+	 * structure, empty subdirectories within that structure may or may not be
+	 * deleted even if the method fails. Furthermore if the destination exists
+	 * and is a file then the file will be replaced if
+	 * {@link java.nio.file.StandardCopyOption#REPLACE_EXISTING} has been set.
+	 * If {@link java.nio.file.StandardCopyOption#ATOMIC_MOVE} has been set the
+	 * rename will be done atomically or fail with an
+	 * {@link java.nio.file.AtomicMoveNotSupportedException}
 	 *
 	 * @param src
 	 *            the old file
@@ -268,10 +268,10 @@ public class FileUtils {
 	 *            the new file
 	 * @param options
 	 *            options to pass to
-	 *            {@link Files#move(java.nio.file.Path, java.nio.file.Path, CopyOption...)}
-	 * @throws AtomicMoveNotSupportedException
+	 *            {@link java.nio.file.Files#move(java.nio.file.Path, java.nio.file.Path, CopyOption...)}
+	 * @throws java.nio.file.AtomicMoveNotSupportedException
 	 *             if file cannot be moved as an atomic file system operation
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.1
 	 */
 	public static void rename(final File src, final File dst,
@@ -314,11 +314,12 @@ public class FileUtils {
 	 *
 	 * @param d
 	 *            directory to be created
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if creation of {@code d} fails. This may occur if {@code d}
 	 *             did exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to create the same directory.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to create the same
+	 *             directory.
 	 */
 	public static void mkdir(final File d)
 			throws IOException {
@@ -333,11 +334,12 @@ public class FileUtils {
 	 * @param skipExisting
 	 *            if {@code true} skip creation of the given directory if it
 	 *            already exists in the file system
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if creation of {@code d} fails. This may occur if {@code d}
 	 *             did exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to create the same directory.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to create the same
+	 *             directory.
 	 */
 	public static void mkdir(final File d, boolean skipExisting)
 			throws IOException {
@@ -357,11 +359,12 @@ public class FileUtils {
 	 *
 	 * @param d
 	 *            directory to be created
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if creation of {@code d} fails. This may occur if {@code d}
 	 *             did exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to create the same directory.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to create the same
+	 *             directory.
 	 */
 	public static void mkdirs(final File d) throws IOException {
 		mkdirs(d, false);
@@ -378,11 +381,12 @@ public class FileUtils {
 	 * @param skipExisting
 	 *            if {@code true} skip creation of the given directory if it
 	 *            already exists in the file system
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if creation of {@code d} fails. This may occur if {@code d}
 	 *             did exist when the method was called. This can therefore
-	 *             cause IOExceptions during race conditions when multiple
-	 *             concurrent threads all try to create the same directory.
+	 *             cause java.io.IOExceptions during race conditions when
+	 *             multiple concurrent threads all try to create the same
+	 *             directory.
 	 */
 	public static void mkdirs(final File d, boolean skipExisting)
 			throws IOException {
@@ -402,12 +406,12 @@ public class FileUtils {
 	 * filesystem activities that might affect the file.
 	 * <p>
 	 * Note: this method should not be used for file-locking, as the resulting
-	 * protocol cannot be made to work reliably. The {@link FileLock} facility
-	 * should be used instead.
+	 * protocol cannot be made to work reliably. The
+	 * {@link java.nio.channels.FileLock} facility should be used instead.
 	 *
 	 * @param f
 	 *            the file to be created
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if the named file already exists or if an I/O error occurred
 	 */
 	public static void createNewFile(File f) throws IOException {
@@ -424,7 +428,7 @@ public class FileUtils {
 	 * @param target
 	 *            the target of the symbolic link
 	 * @return the path to the symbolic link
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	public static Path createSymLink(File path, String target)
@@ -447,9 +451,12 @@ public class FileUtils {
 	}
 
 	/**
+	 * Read target path of the symlink.
+	 *
 	 * @param path
+	 *            a {@link java.io.File} object.
 	 * @return target path of the symlink, or null if it is not a symbolic link
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.0
 	 */
 	public static String readSymLink(File path) throws IOException {
@@ -468,11 +475,13 @@ public class FileUtils {
 	 * Create a temporary directory.
 	 *
 	 * @param prefix
+	 *            prefix string
 	 * @param suffix
+	 *            suffix string
 	 * @param dir
 	 *            The parent dir, can be null to use system default temp dir.
 	 * @return the temp dir created.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.4
 	 */
 	public static File createTempDir(String prefix, String suffix, File dir)
@@ -491,18 +500,19 @@ public class FileUtils {
 
 
 	/**
+	 * Relativize a path
+	 *
 	 * @deprecated Use the more-clearly-named
-	 *             {@link FileUtils#relativizeNativePath(String, String)}
+	 *             {@link org.eclipse.jgit.util.FileUtils#relativizeNativePath(String, String)}
 	 *             instead, or directly call
-	 *             {@link FileUtils#relativizePath(String, String, String, boolean)}
+	 *             {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}
 	 *
 	 *             Expresses <code>other</code> as a relative file path from
 	 *             <code>base</code>. File-separator and case sensitivity are
 	 *             based on the current file system.
 	 *
 	 *             See also
-	 *             {@link FileUtils#relativizePath(String, String, String, boolean)}.
-	 *
+	 *             {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}.
 	 * @param base
 	 *            Base path
 	 * @param other
@@ -516,15 +526,17 @@ public class FileUtils {
 	}
 
 	/**
-	 * Expresses <code>other</code> as a relative file path from <code>base</code>.
-	 * File-separator and case sensitivity are based on the current file system.
+	 * Expresses <code>other</code> as a relative file path from
+	 * <code>base</code>. File-separator and case sensitivity are based on the
+	 * current file system.
 	 *
-	 * See also {@link FileUtils#relativizePath(String, String, String, boolean)}.
+	 * See also
+	 * {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}.
 	 *
 	 * @param base
 	 *            Base path
 	 * @param other
-	 *             Destination path
+	 *            Destination path
 	 * @return Relative path from <code>base</code> to <code>other</code>
 	 * @since 4.8
 	 */
@@ -533,15 +545,17 @@ public class FileUtils {
 	}
 
 	/**
-	 * Expresses <code>other</code> as a relative file path from <code>base</code>.
-	 * File-separator and case sensitivity are based on Git's internal representation of files (which matches Unix).
+	 * Expresses <code>other</code> as a relative file path from
+	 * <code>base</code>. File-separator and case sensitivity are based on Git's
+	 * internal representation of files (which matches Unix).
 	 *
-	 * See also {@link FileUtils#relativizePath(String, String, String, boolean)}.
+	 * See also
+	 * {@link org.eclipse.jgit.util.FileUtils#relativizePath(String, String, String, boolean)}.
 	 *
 	 * @param base
 	 *            Base path
 	 * @param other
-	 *             Destination path
+	 *            Destination path
 	 * @return Relative path from <code>base</code> to <code>other</code>
 	 * @since 4.8
 	 */
@@ -620,6 +634,7 @@ public class FileUtils {
 	 * Determine if an IOException is a Stale NFS File Handle
 	 *
 	 * @param ioe
+	 *            an {@link java.io.IOException} object.
 	 * @return a boolean true if the IOException is a Stale NFS FIle Handle
 	 * @since 4.1
 	 */
@@ -635,6 +650,7 @@ public class FileUtils {
 	 * File Handle
 	 *
 	 * @param throwable
+	 *            a {@link java.lang.Throwable} object.
 	 * @return a boolean true if the throwable or a cause in its causal chain is
 	 *         a Stale NFS File Handle
 	 * @since 4.7
@@ -697,9 +713,13 @@ public class FileUtils {
 	}
 
 	/**
+	 * Set a file hidden (on Windows)
+	 *
 	 * @param file
+	 *            a {@link java.io.File} object.
 	 * @param hidden
-	 * @throws IOException
+	 *            a boolean.
+	 * @throws java.io.IOException
 	 * @since 4.1
 	 */
 	public static void setHidden(File file, boolean hidden) throws IOException {
@@ -708,9 +728,12 @@ public class FileUtils {
 	}
 
 	/**
+	 * Get file length
+	 *
 	 * @param file
+	 *            a {@link java.io.File}.
 	 * @return length of the given file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.1
 	 */
 	public static long getLength(File file) throws IOException {
@@ -740,8 +763,11 @@ public class FileUtils {
 	}
 
 	/**
+	 * Whether the given file can be executed.
+	 *
 	 * @param file
-	 * @return {@code true} if the given file can be executed
+	 *            a {@link java.io.File} object.
+	 * @return {@code true} if the given file can be executed.
 	 * @since 4.1
 	 */
 	public static boolean canExecute(File file) {
@@ -783,9 +809,13 @@ public class FileUtils {
 	}
 
 	/**
+	 * Get file system attributes for the given file.
+	 *
 	 * @param fs
+	 *            a {@link org.eclipse.jgit.util.FS} object.
 	 * @param file
-	 * @return file system attributes for the given file
+	 *            a {@link java.io.File}.
+	 * @return file system attributes for the given file.
 	 * @since 4.1
 	 */
 	public static Attributes getFileAttributesPosix(FS fs, File file) {
@@ -816,8 +846,12 @@ public class FileUtils {
 	}
 
 	/**
+	 * NFC normalize a file (on Mac), otherwise do nothing
+	 *
 	 * @param file
-	 * @return on Mac: NFC normalized {@link File}, otherwise the passed file
+	 *            a {@link java.io.File}.
+	 * @return on Mac: NFC normalized {@link java.io.File}, otherwise the passed
+	 *         file
 	 * @since 4.1
 	 */
 	public static File normalize(File file) {
@@ -832,7 +866,10 @@ public class FileUtils {
 	}
 
 	/**
+	 * On Mac: get NFC normalized form of given name, otherwise the given name.
+	 *
 	 * @param name
+	 *            a {@link java.lang.String} object.
 	 * @return on Mac: NFC normalized form of given name
 	 * @since 4.1
 	 */
@@ -846,16 +883,16 @@ public class FileUtils {
 	}
 
 	/**
-	 * Best-effort variation of {@link File#getCanonicalFile()} returning the
-	 * input file if the file cannot be canonicalized instead of throwing
-	 * {@link IOException}.
+	 * Best-effort variation of {@link java.io.File#getCanonicalFile()}
+	 * returning the input file if the file cannot be canonicalized instead of
+	 * throwing {@link java.io.IOException}.
 	 *
 	 * @param file
 	 *            to be canonicalized; may be {@code null}
 	 * @return canonicalized file, or the unchanged input file if
 	 *         canonicalization failed or if {@code file == null}
-	 * @throws SecurityException
-	 *             if {@link File#getCanonicalFile()} throws one
+	 * @throws java.lang.SecurityException
+	 *             if {@link java.io.File#getCanonicalFile()} throws one
 	 * @since 4.2
 	 */
 	public static File canonicalize(File file) {
@@ -873,6 +910,7 @@ public class FileUtils {
 	 * Convert a path to String, replacing separators as necessary.
 	 *
 	 * @param file
+	 *            a {@link java.io.File}.
 	 * @return file's path as a String
 	 * @since 4.10
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateFormatter.java

@@ -54,7 +54,8 @@ import org.eclipse.jgit.lib.PersonIdent;
  * A utility for formatting dates according to the Git log.date formats plus
  * extensions.
  * <p>
- * The enum {@link Format} defines the available types.
+ * The enum {@link org.eclipse.jgit.util.GitDateFormatter.Format} defines the
+ * available types.
  */
 public class GitDateFormatter {
 
@@ -119,6 +120,8 @@ public class GitDateFormatter {
 	 * Create a new Git oriented date formatter
 	 *
 	 * @param format
+	 *            a {@link org.eclipse.jgit.util.GitDateFormatter.Format}
+	 *            object.
 	 */
 	public GitDateFormatter(Format format) {
 		this.format = format;
@@ -159,6 +162,7 @@ public class GitDateFormatter {
 	 * specification.
 	 *
 	 * @param ident
+	 *            a {@link org.eclipse.jgit.lib.PersonIdent} object.
 	 * @return formatted version of date, time and time zone
 	 */
 	@SuppressWarnings("boxing")

org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateParser.java

@@ -55,7 +55,7 @@ import java.util.Map;
 import org.eclipse.jgit.internal.JGitText;
 
 /**
- * Parses strings with time and date specifications into {@link Date}.
+ * Parses strings with time and date specifications into {@link java.util.Date}.
  *
  * When git needs to parse strings specified by the user this parser can be
  * used. One example is the parsing of the config parameter gc.pruneexpire. The
@@ -134,16 +134,17 @@ public class GitDateParser {
 	}
 
 	/**
-	 * Parses a string into a {@link Date} using the default locale. Since this
-	 * parser also supports relative formats (e.g. "yesterday") the caller can
-	 * specify the reference date. These types of strings can be parsed:
+	 * Parses a string into a {@link java.util.Date} using the default locale.
+	 * Since this parser also supports relative formats (e.g. "yesterday") the
+	 * caller can specify the reference date. These types of strings can be
+	 * parsed:
 	 * <ul>
 	 * <li>"never"</li>
 	 * <li>"now"</li>
 	 * <li>"yesterday"</li>
 	 * <li>"(x) years|months|weeks|days|hours|minutes|seconds ago"<br>
-	 * Multiple specs can be combined like in "2 weeks 3 days ago". Instead of
-	 * ' ' one can use '.' to seperate the words</li>
+	 * Multiple specs can be combined like in "2 weeks 3 days ago". Instead of '
+	 * ' one can use '.' to seperate the words</li>
 	 * <li>"yyyy-MM-dd HH:mm:ss Z" (ISO)</li>
 	 * <li>"EEE, dd MMM yyyy HH:mm:ss Z" (RFC)</li>
 	 * <li>"yyyy-MM-dd"</li>
@@ -161,11 +162,12 @@ public class GitDateParser {
 	 *            formats. E.g. if baseDate is "25.8.2012" then parsing of the
 	 *            string "1 week ago" would result in a date corresponding to
 	 *            "18.8.2012". This is used when a JGit command calls this
-	 *            parser often but wants a consistent starting point for calls.<br>
+	 *            parser often but wants a consistent starting point for
+	 *            calls.<br>
 	 *            If set to <code>null</code> then the current time will be used
 	 *            instead.
-	 * @return the parsed {@link Date}
-	 * @throws ParseException
+	 * @return the parsed {@link java.util.Date}
+	 * @throws java.text.ParseException
 	 *             if the given dateStr was not recognized
 	 */
 	public static Date parse(String dateStr, Calendar now)
@@ -174,16 +176,17 @@ public class GitDateParser {
 	}
 
 	/**
-	 * Parses a string into a {@link Date} using the given locale. Since this
-	 * parser also supports relative formats (e.g. "yesterday") the caller can
-	 * specify the reference date. These types of strings can be parsed:
+	 * Parses a string into a {@link java.util.Date} using the given locale.
+	 * Since this parser also supports relative formats (e.g. "yesterday") the
+	 * caller can specify the reference date. These types of strings can be
+	 * parsed:
 	 * <ul>
 	 * <li>"never"</li>
 	 * <li>"now"</li>
 	 * <li>"yesterday"</li>
 	 * <li>"(x) years|months|weeks|days|hours|minutes|seconds ago"<br>
-	 * Multiple specs can be combined like in "2 weeks 3 days ago". Instead of
-	 * ' ' one can use '.' to seperate the words</li>
+	 * Multiple specs can be combined like in "2 weeks 3 days ago". Instead of '
+	 * ' one can use '.' to seperate the words</li>
 	 * <li>"yyyy-MM-dd HH:mm:ss Z" (ISO)</li>
 	 * <li>"EEE, dd MMM yyyy HH:mm:ss Z" (RFC)</li>
 	 * <li>"yyyy-MM-dd"</li>
@@ -201,13 +204,14 @@ public class GitDateParser {
 	 *            formats. E.g. if baseDate is "25.8.2012" then parsing of the
 	 *            string "1 week ago" would result in a date corresponding to
 	 *            "18.8.2012". This is used when a JGit command calls this
-	 *            parser often but wants a consistent starting point for calls.<br>
+	 *            parser often but wants a consistent starting point for
+	 *            calls.<br>
 	 *            If set to <code>null</code> then the current time will be used
 	 *            instead.
 	 * @param locale
 	 *            locale to be used to parse the date string
-	 * @return the parsed {@link Date}
-	 * @throws ParseException
+	 * @return the parsed {@link java.util.Date}
+	 * @throws java.text.ParseException
 	 *             if the given dateStr was not recognized
 	 * @since 3.2
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/Holder.java

@@ -45,14 +45,15 @@ package org.eclipse.jgit.util;
  * Holder of an object.
  *
  * @param <T>
- *            the type of value held by this {@link Holder}
- *
+ *            the type of value held by this {@link org.eclipse.jgit.util.Holder}
  * @since 4.3
  */
 public class Holder<T> {
 	private T value;
 
 	/**
+	 * <p>Constructor for Holder.</p>
+	 *
 	 * @param value
 	 *            is the initial value that is {@link #set(Object)}
 	 */
@@ -61,15 +62,20 @@ public class Holder<T> {
 	}
 
 	/**
-	 * @return the value held by this {@link Holder}
+	 * Get the value held by this {@link org.eclipse.jgit.util.Holder}
+	 *
+	 * @return the value held by this {@link org.eclipse.jgit.util.Holder}
 	 */
 	public T get() {
 		return value;
 	}
 
 	/**
+	 * Set a new value held by this {@link org.eclipse.jgit.util.Holder}
+	 *
 	 * @param value
-	 *            to be set as new value held by this {@link Holder}
+	 *            to be set as new value held by this
+	 *            {@link org.eclipse.jgit.util.Holder}
 	 */
 	public void set(T value) {
 		this.value = value;

org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java

@@ -65,7 +65,9 @@ import javax.net.ssl.X509TrustManager;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.transport.http.HttpConnection;
 
-/** Extra utilities to support usage of HTTP. */
+/**
+ * Extra utilities to support usage of HTTP.
+ */
 public class HttpSupport {
 	/** The {@code GET} HTTP method. */
 	public static final String METHOD_GET = "GET"; //$NON-NLS-1$
@@ -192,8 +194,9 @@ public class HttpSupport {
 	 * @param c
 	 *            connection the code should be obtained from.
 	 * @return r HTTP status code, usually 200 to indicate success. See
-	 *         {@link HttpConnection} for other defined constants.
-	 * @throws IOException
+	 *         {@link org.eclipse.jgit.transport.http.HttpConnection} for other
+	 *         defined constants.
+	 * @throws java.io.IOException
 	 *             communications error prevented obtaining the response code.
 	 * @since 3.3
 	 */
@@ -220,8 +223,9 @@ public class HttpSupport {
 	 * @param c
 	 *            connection the code should be obtained from.
 	 * @return r HTTP status code, usually 200 to indicate success. See
-	 *         {@link HttpConnection} for other defined constants.
-	 * @throws IOException
+	 *         {@link org.eclipse.jgit.transport.http.HttpConnection} for other
+	 *         defined constants.
+	 * @throws java.io.IOException
 	 *             communications error prevented obtaining the response code.
 	 */
 	public static int response(final java.net.HttpURLConnection c)
@@ -248,7 +252,7 @@ public class HttpSupport {
 	 * @param headerName
 	 *            the header name
 	 * @return the header value
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             communications error prevented obtaining the header.
 	 * @since 4.7
 	 */
@@ -265,7 +269,7 @@ public class HttpSupport {
 	 * @param u
 	 *            location of the server caller wants to talk to.
 	 * @return proxy to communicate with the supplied URL.
-	 * @throws ConnectException
+	 * @throws java.net.ConnectException
 	 *             the proxy could not be computed as the supplied URL could not
 	 *             be read. This failure should never occur.
 	 */
@@ -285,7 +289,9 @@ public class HttpSupport {
 	 * Disable SSL and hostname verification for given HTTP connection
 	 *
 	 * @param conn
-	 * @throws IOException
+	 *            a {@link org.eclipse.jgit.transport.http.HttpConnection}
+	 *            object.
+	 * @throws java.io.IOException
 	 * @since 4.3
 	 */
 	public static void disableSslVerify(HttpConnection conn)

org.eclipse.jgit/src/org/eclipse/jgit/util/IO.java

@@ -71,9 +71,9 @@ public class IO {
 	 * @param path
 	 *            location of the file to read.
 	 * @return complete contents of the requested local file.
-	 * @throws FileNotFoundException
+	 * @throws java.io.FileNotFoundException
 	 *             the file does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file exists, but its contents cannot be read.
 	 */
 	public static final byte[] readFully(final File path)
@@ -91,9 +91,9 @@ public class IO {
 	 *            only the first limit number of bytes are returned
 	 * @return complete contents of the requested local file. If the contents
 	 *         exceeds the limit, then only the limit is returned.
-	 * @throws FileNotFoundException
+	 * @throws java.io.FileNotFoundException
 	 *             the file does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file exists, but its contents cannot be read.
 	 */
 	public static final byte[] readSome(final File path, final int limit)
@@ -131,9 +131,9 @@ public class IO {
 	 *            maximum number of bytes to read, if the file is larger than
 	 *            this limit an IOException is thrown.
 	 * @return complete contents of the requested local file.
-	 * @throws FileNotFoundException
+	 * @throws java.io.FileNotFoundException
 	 *             the file does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file exists, but its contents cannot be read.
 	 */
 	public static final byte[] readFully(final File path, final int max)
@@ -199,7 +199,7 @@ public class IO {
 	 *         on obtaining the underlying array for efficient data access. If
 	 *         {@code sizeHint} was too large, the array may be over-allocated,
 	 *         resulting in {@code limit() < array().length}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the stream.
 	 */
 	public static ByteBuffer readWholeStream(InputStream in, int sizeHint)
@@ -238,7 +238,7 @@ public class IO {
 	 *            number of bytes that must be read.
 	 * @throws EOFException
 	 *             the stream ended before dst was fully populated.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the stream.
 	 */
 	public static void readFully(final InputStream fd, final byte[] dst,
@@ -264,7 +264,7 @@ public class IO {
 	 * @param len
 	 *            number of bytes that should be read.
 	 * @return number of bytes actually read.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the channel.
 	 */
 	public static int read(ReadableByteChannel channel, byte[] dst, int off,
@@ -293,7 +293,7 @@ public class IO {
 	 * @param off
 	 *            position within the buffer to start writing to.
 	 * @return number of bytes in buffer or stream, whichever is shortest
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the stream.
 	 */
 	public static int readFully(InputStream fd, byte[] dst, int off)
@@ -322,7 +322,7 @@ public class IO {
 	 * @throws EOFException
 	 *             the stream ended before the requested number of bytes were
 	 *             skipped.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the stream.
 	 */
 	public static void skipFully(final InputStream fd, long toSkip)
@@ -384,7 +384,7 @@ public class IO {
 	 *            hint for buffer sizing; 0 or negative for default.
 	 * @return the next line from the input, always ending in {@code \n} unless
 	 *         EOF was reached.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             there was an error reading from the stream.
 	 * @since 4.1
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/IntList.java

@@ -44,13 +44,17 @@
 
 package org.eclipse.jgit.util;
 
-/** A more efficient List<Integer> using a primitive integer array. */
+/**
+ * A more efficient List<Integer> using a primitive integer array.
+ */
 public class IntList {
 	private int[] entries;
 
 	private int count;
 
-	/** Create an empty list with a default capacity. */
+	/**
+	 * Create an empty list with a default capacity.
+	 */
 	public IntList() {
 		this(10);
 	}
@@ -65,7 +69,11 @@ public class IntList {
 		entries = new int[capacity];
 	}
 
-	/** @return number of entries in this list */
+	/**
+	 * Get number of entries in this list.
+	 *
+	 * @return number of entries in this list.
+	 */
 	public int size() {
 		return count;
 	}
@@ -86,10 +94,12 @@ public class IntList {
 	}
 
 	/**
+	 * Get the value at the specified index
+	 *
 	 * @param i
 	 *            index to read, must be in the range [0, {@link #size()}).
 	 * @return the number at the specified index
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             the index outside the valid range
 	 */
 	public int get(final int i) {
@@ -98,7 +108,9 @@ public class IntList {
 		return entries[i];
 	}
 
-	/** Empty this list */
+	/**
+	 * Empty this list
+	 */
 	public void clear() {
 		count = 0;
 	}
@@ -153,6 +165,7 @@ public class IntList {
 		entries = n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		final StringBuilder r = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/util/LongList.java

@@ -46,13 +46,17 @@ package org.eclipse.jgit.util;
 
 import java.util.Arrays;
 
-/** A more efficient List<Long> using a primitive long array. */
+/**
+ * A more efficient List<Long> using a primitive long array.
+ */
 public class LongList {
 	private long[] entries;
 
 	private int count;
 
-	/** Create an empty list with a default capacity. */
+	/**
+	 * Create an empty list with a default capacity.
+	 */
 	public LongList() {
 		this(10);
 	}
@@ -67,16 +71,22 @@ public class LongList {
 		entries = new long[capacity];
 	}
 
-	/** @return number of entries in this list */
+	/**
+	 * Get number of entries in this list
+	 *
+	 * @return number of entries in this list
+	 */
 	public int size() {
 		return count;
 	}
 
 	/**
+	 * Get the value at the specified index
+	 *
 	 * @param i
 	 *            index to read, must be in the range [0, {@link #size()}).
 	 * @return the number at the specified index
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             the index outside the valid range
 	 */
 	public long get(final int i) {
@@ -99,7 +109,9 @@ public class LongList {
 		return false;
 	}
 
-	/** Empty this list */
+	/**
+	 * Clear this list
+	 */
 	public void clear() {
 		count = 0;
 	}
@@ -148,7 +160,9 @@ public class LongList {
 			add(val);
 	}
 
-	/** Sort the list of longs according to their natural ordering. */
+	/**
+	 * Sort the list of longs according to their natural ordering.
+	 */
 	public void sort() {
 		Arrays.sort(entries, 0, count);
 	}
@@ -159,6 +173,7 @@ public class LongList {
 		entries = n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		final StringBuilder r = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/util/LongMap.java

@@ -61,13 +61,17 @@ public class LongMap<V> {
 	/** Next {@link #size} to trigger a {@link #grow()}. */
 	private int growAt;
 
-	/** Initialize an empty LongMap. */
+	/**
+	 * Initialize an empty LongMap.
+	 */
 	public LongMap() {
 		table = createArray(64);
 		growAt = (int) (table.length * LOAD_FACTOR);
 	}
 
 	/**
+	 * Whether {@code key} is present in the map.
+	 *
 	 * @param key
 	 *            the key to find.
 	 * @return {@code true} if {@code key} is present in the map.
@@ -77,9 +81,11 @@ public class LongMap<V> {
 	}
 
 	/**
+	 * Get value for this {@code key}
+	 *
 	 * @param key
 	 *            the key to find.
-	 * @return stored value of the key, or {@code null}.
+	 * @return stored value for this key, or {@code null}.
 	 */
 	public V get(long key) {
 		for (Node<V> n = table[index(key)]; n != null; n = n.next) {
@@ -90,6 +96,8 @@ public class LongMap<V> {
 	}
 
 	/**
+	 * Remove an entry from the map
+	 *
 	 * @param key
 	 *            key to remove from the map.
 	 * @return old value of the key, or {@code null}.
@@ -113,6 +121,8 @@ public class LongMap<V> {
 	}
 
 	/**
+	 * Put a new entry into the map
+	 *
 	 * @param key
 	 *            key to store {@code value} under.
 	 * @param value

org.eclipse.jgit/src/org/eclipse/jgit/util/MutableInteger.java

@@ -43,7 +43,9 @@
 
 package org.eclipse.jgit.util;
 
-/** A boxed integer that can be modified. */
+/**
+ * A boxed integer that can be modified.
+ */
 public final class MutableInteger {
 	/** Current value of this boxed value. */
 	public int value;

org.eclipse.jgit/src/org/eclipse/jgit/util/NB.java

@@ -43,7 +43,9 @@
 
 package org.eclipse.jgit.util;
 
-/** Conversion utilities for network byte order handling. */
+/**
+ * Conversion utilities for network byte order handling.
+ */
 public final class NB {
 	/**
 	 * Compare a 32 bit unsigned integer stored in a 32 bit signed integer.

org.eclipse.jgit/src/org/eclipse/jgit/util/ProcessResult.java

@@ -86,6 +86,8 @@ public class ProcessResult {
 	}
 
 	/**
+	 * <p>Constructor for ProcessResult.</p>
+	 *
 	 * @param exitCode
 	 *            Exit code of the process.
 	 * @param status
@@ -97,6 +99,8 @@ public class ProcessResult {
 	}
 
 	/**
+	 * Get exit code of the process.
+	 *
 	 * @return The exit code of the process.
 	 */
 	public int getExitCode() {
@@ -104,6 +108,8 @@ public class ProcessResult {
 	}
 
 	/**
+	 * Get the status of the process' execution.
+	 *
 	 * @return The status of the process' execution.
 	 */
 	public Status getStatus() {
@@ -111,6 +117,8 @@ public class ProcessResult {
 	}
 
 	/**
+	 * Whether the execution occurred and resulted in an error
+	 *
 	 * @return <code>true</code> if the execution occurred and resulted in a
 	 *         return code different from 0, <code>false</code> otherwise.
 	 * @since 4.0

org.eclipse.jgit/src/org/eclipse/jgit/util/QuotedString.java

@@ -47,7 +47,9 @@ import java.util.Arrays;
 
 import org.eclipse.jgit.lib.Constants;
 
-/** Utility functions related to quoted string handling. */
+/**
+ * Utility functions related to quoted string handling.
+ */
 public abstract class QuotedString {
 	/** Quoting style that obeys the rules Git applies to file names */
 	public static final GitPathStyle GIT_PATH = new GitPathStyle();

org.eclipse.jgit/src/org/eclipse/jgit/util/RawCharSequence.java

@@ -74,21 +74,25 @@ public final class RawCharSequence implements CharSequence {
 		endPtr = end;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public char charAt(final int index) {
 		return (char) (buffer[startPtr + index] & 0xff);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int length() {
 		return endPtr - startPtr;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public CharSequence subSequence(final int start, final int end) {
 		return new RawCharSequence(buffer, startPtr + start, startPtr + end);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		final int n = length();

org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java

@@ -66,7 +66,9 @@ import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.PersonIdent;
 
-/** Handy utility functions to parse raw object contents. */
+/**
+ * Handy utility functions to parse raw object contents.
+ */
 public final class RawParseUtils {
 	/**
 	 * UTF-8 charset constant.
@@ -306,7 +308,7 @@ public final class RawParseUtils {
 	 * @param p
 	 *            first position within the buffer to parse.
 	 * @return the integer value.
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             if the string is not hex formatted.
 	 */
 	public static final int parseHexInt16(final byte[] bs, final int p) {
@@ -336,7 +338,7 @@ public final class RawParseUtils {
 	 * @param p
 	 *            first position within the buffer to parse.
 	 * @return the integer value.
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             if the string is not hex formatted.
 	 */
 	public static final int parseHexInt32(final byte[] bs, final int p) {
@@ -377,7 +379,7 @@ public final class RawParseUtils {
 	 * @param p
 	 *            first position within the buffer to parse.
 	 * @return the integer value.
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             if the string is not hex formatted.
 	 * @since 4.3
 	 */
@@ -437,7 +439,7 @@ public final class RawParseUtils {
 	 * @param digit
 	 *            hex character to parse.
 	 * @return numeric value, in the range 0-15.
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             if the input digit is not a valid hex digit.
 	 */
 	public static final int parseHexInt4(final byte digit) {
@@ -610,7 +612,7 @@ public final class RawParseUtils {
 	 * Index the region between <code>[ptr, end)</code> to find line starts.
 	 * <p>
 	 * The returned list is 1 indexed. Index 0 contains
-	 * {@link Integer#MIN_VALUE} to pad the list out.
+	 * {@link java.lang.Integer#MIN_VALUE} to pad the list out.
 	 * <p>
 	 * Using a 1 indexed list means that line numbers can be directly accessed
 	 * from the list, so <code>list.get(1)</code> (aka get line 1) returns
@@ -619,8 +621,8 @@ public final class RawParseUtils {
 	 * The last element (index <code>map.size()-1</code>) always contains
 	 * <code>end</code>.
 	 * <p>
-	 * If the data contains a '\0' anywhere, the whole region is considered binary
-	 * and a LineMap corresponding to a single line is returned.
+	 * If the data contains a '\0' anywhere, the whole region is considered
+	 * binary and a LineMap corresponding to a single line is returned.
 	 * </p>
 	 *
 	 * @param buf
@@ -1076,7 +1078,7 @@ public final class RawParseUtils {
 	 *            data from.
 	 * @return a string representation of the range <code>[start,end)</code>,
 	 *         after decoding the region through the specified character set.
-	 * @throws CharacterCodingException
+	 * @throws java.nio.charset.CharacterCodingException
 	 *             the input is not in any of the tested character sets.
 	 */
 	public static String decodeNoFallback(final Charset cs,
@@ -1222,13 +1224,15 @@ public final class RawParseUtils {
 	}
 
 	/**
+	 * Get last index of {@code ch} in raw, trimming spaces.
+	 *
 	 * @param raw
 	 *            buffer to scan.
 	 * @param ch
 	 *            character to find.
 	 * @param pos
 	 *            starting position.
-	 * @return last index of ch in raw, trimming spaces.
+	 * @return last index of {@code ch} in raw, trimming spaces.
 	 * @since 4.1
 	 */
 	public static int lastIndexOfTrim(byte[] raw, char ch, int pos) {

org.eclipse.jgit/src/org/eclipse/jgit/util/RawSubStringPattern.java

@@ -131,6 +131,7 @@ public class RawSubStringPattern {
 		return needleString;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return pattern();

org.eclipse.jgit/src/org/eclipse/jgit/util/RefList.java

@@ -71,9 +71,9 @@ public class RefList<T extends Ref> implements Iterable<Ref> {
 	private static final RefList<Ref> EMPTY = new RefList<>(new Ref[0], 0);
 
 	/**
+	 * Create an empty unmodifiable reference list.
+	 *
 	 * @return an empty unmodifiable reference list.
-	 * @param <T>
-	 *            the type of reference being stored in the collection.
 	 */
 	@SuppressWarnings("unchecked")
 	public static <T extends Ref> RefList<T> emptyList() {
@@ -100,6 +100,7 @@ public class RefList<T extends Ref> implements Iterable<Ref> {
 		this.cnt = src.cnt;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<Ref> iterator() {
 		return new Iterator<Ref>() {
@@ -124,18 +125,30 @@ public class RefList<T extends Ref> implements Iterable<Ref> {
 		};
 	}
 
-	/** @return this cast as an immutable, standard {@link java.util.List}. */
+	/**
+	 * Cast {@code this} as an immutable, standard {@link java.util.List}.
+	 *
+	 * @return {@code this} as an immutable, standard {@link java.util.List}.
+	 */
 	public final List<Ref> asList() {
 		final List<Ref> r = Arrays.asList(list).subList(0, cnt);
 		return Collections.unmodifiableList(r);
 	}
 
-	/** @return number of items in this list. */
+	/**
+	 * Get number of items in this list.
+	 *
+	 * @return number of items in this list.
+	 */
 	public final int size() {
 		return cnt;
 	}
 
-	/** @return true if the size of this list is 0. */
+	/**
+	 * Get if this list is empty.
+	 *
+	 * @return true if the size of this list is 0.
+	 */
 	public final boolean isEmpty() {
 		return cnt == 0;
 	}
@@ -303,6 +316,7 @@ public class RefList<T extends Ref> implements Iterable<Ref> {
 		return add(idx, ref);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		StringBuilder r = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/util/RefMap.java

@@ -59,17 +59,19 @@ import org.eclipse.jgit.lib.RefComparator;
  * Specialized Map to present a {@code RefDatabase} namespace.
  * <p>
  * Although not declared as a {@link java.util.SortedMap}, iterators from this
- * map's projections always return references in {@link RefComparator} ordering.
- * The map's internal representation is a sorted array of {@link Ref} objects,
+ * map's projections always return references in
+ * {@link org.eclipse.jgit.lib.RefComparator} ordering. The map's internal
+ * representation is a sorted array of {@link org.eclipse.jgit.lib.Ref} objects,
  * which means lookup and replacement is O(log N), while insertion and removal
  * can be as expensive as O(N + log N) while the list expands or contracts.
  * Since this is not a general map implementation, all entries must be keyed by
  * the reference name.
  * <p>
  * This class is really intended as a helper for {@code RefDatabase}, which
- * needs to perform a merge-join of three sorted {@link RefList}s in order to
- * present the unified namespace of the packed-refs file, the loose refs/
- * directory tree, and the resolved form of any symbolic references.
+ * needs to perform a merge-join of three sorted
+ * {@link org.eclipse.jgit.util.RefList}s in order to present the unified
+ * namespace of the packed-refs file, the loose refs/ directory tree, and the
+ * resolved form of any symbolic references.
  */
 public class RefMap extends AbstractMap<String, Ref> {
 	/**
@@ -109,7 +111,9 @@ public class RefMap extends AbstractMap<String, Ref> {
 
 	private Set<Entry<String, Ref>> entrySet;
 
-	/** Construct an empty map with a small initial capacity. */
+	/**
+	 * Construct an empty map with a small initial capacity.
+	 */
 	public RefMap() {
 		prefix = ""; //$NON-NLS-1$
 		packed = RefList.emptyList();
@@ -145,11 +149,13 @@ public class RefMap extends AbstractMap<String, Ref> {
 		this.resolved = (RefList<Ref>) resolved;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean containsKey(Object name) {
 		return get(name) != null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref get(Object key) {
 		String name = toRefName((String) key);
@@ -161,6 +167,7 @@ public class RefMap extends AbstractMap<String, Ref> {
 		return ref;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref put(final String keyName, Ref value) {
 		String name = toRefName(keyName);
@@ -189,6 +196,7 @@ public class RefMap extends AbstractMap<String, Ref> {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Ref remove(Object key) {
 		String name = toRefName((String) key);
@@ -212,11 +220,13 @@ public class RefMap extends AbstractMap<String, Ref> {
 		return res;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isEmpty() {
 		return entrySet().isEmpty();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Set<Entry<String, Ref>> entrySet() {
 		if (entrySet == null) {
@@ -258,6 +268,7 @@ public class RefMap extends AbstractMap<String, Ref> {
 		return entrySet;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		StringBuilder r = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/util/RelativeDateFormatter.java

@@ -67,10 +67,14 @@ public class RelativeDateFormatter {
 	final static long YEAR_IN_MILLIS = 365 * DAY_IN_MILLIS;
 
 	/**
+	 * Get age of given {@link java.util.Date} compared to now formatted in the
+	 * same relative format as returned by {@code git log --relative-date}
+	 *
 	 * @param when
-	 *            {@link Date} to format
-	 * @return age of given {@link Date} compared to now formatted in the same
-	 *         relative format as returned by {@code git log --relative-date}
+	 *            {@link java.util.Date} to format
+	 * @return age of given {@link java.util.Date} compared to now formatted in
+	 *         the same relative format as returned by
+	 *         {@code git log --relative-date}
 	 */
 	@SuppressWarnings("boxing")
 	public static String format(Date when) {

org.eclipse.jgit/src/org/eclipse/jgit/util/StringUtils.java

@@ -48,7 +48,9 @@ import java.util.Collection;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** Miscellaneous string comparison utility methods. */
+/**
+ * Miscellaneous string comparison utility methods.
+ */
 public final class StringUtils {
 	private static final char[] LC;
 
@@ -102,10 +104,12 @@ public final class StringUtils {
 	 *
 	 * <p>
 	 * Capitalizes a String changing the first letter to title case as per
-	 * {@link Character#toTitleCase(char)}. No other letters are changed.
+	 * {@link java.lang.Character#toTitleCase(char)}. No other letters are
+	 * changed.
 	 * </p>
 	 *
-	 * A <code>null</code> input String returns <code>null</code>.</p>
+	 * A <code>null</code> input String returns <code>null</code>.
+	 * </p>
 	 *
 	 * @param str
 	 *            the String to capitalize, may be null
@@ -156,9 +160,8 @@ public final class StringUtils {
 	 *            first string to compare.
 	 * @param b
 	 *            second string to compare.
-	 * @return negative, zero or positive if a sorts before, is equal to, or
-	 *         sorts after b.
 	 * @since 2.0
+	 * @return an int.
 	 */
 	public static int compareIgnoreCase(String a, String b) {
 		for (int i = 0; i < a.length() && i < b.length(); i++) {
@@ -179,9 +182,8 @@ public final class StringUtils {
 	 *            first string to compare.
 	 * @param b
 	 *            second string to compare.
-	 * @return negative, zero or positive if a sorts before, is equal to, or
-	 *         sorts after b.
 	 * @since 2.0
+	 * @return an int.
 	 */
 	public static int compareWithCase(String a, String b) {
 		for (int i = 0; i < a.length() && i < b.length(); i++) {
@@ -199,7 +201,7 @@ public final class StringUtils {
 	 * @param stringValue
 	 *            the string to parse.
 	 * @return the boolean interpretation of {@code value}.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             if {@code value} is not recognized as one of the standard
 	 *             boolean names.
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java

@@ -151,12 +151,18 @@ public abstract class SystemReader {
 
 	private static SystemReader INSTANCE = DEFAULT;
 
-	/** @return the live instance to read system properties. */
+	/**
+	 * Get time since epoch, with up to millisecond resolution.
+	 *
+	 * @return time since epoch, with up to millisecond resolution.
+	 */
 	public static SystemReader getInstance() {
 		return INSTANCE;
 	}
 
 	/**
+	 * Set the new instance to use when accessing properties.
+	 *
 	 * @param newReader
 	 *            the new instance to use when accessing properties, or null for
 	 *            the default instance.
@@ -201,18 +207,26 @@ public abstract class SystemReader {
 	public abstract String getHostname();
 
 	/**
-	 * @param variable system variable to read
+	 * Get value of the system variable
+	 *
+	 * @param variable
+	 *            system variable to read
 	 * @return value of the system variable
 	 */
 	public abstract String getenv(String variable);
 
 	/**
-	 * @param key of the system property to read
+	 * Get value of the system property
+	 *
+	 * @param key
+	 *            of the system property to read
 	 * @return value of the system property
 	 */
 	public abstract String getProperty(String key);
 
 	/**
+	 * Open the git configuration found in the user home
+	 *
 	 * @param parent
 	 *            a config with values not found directly in the returned config
 	 * @param fs
@@ -223,6 +237,8 @@ public abstract class SystemReader {
 	public abstract FileBasedConfig openUserConfig(Config parent, FS fs);
 
 	/**
+	 * Open the gitonfig configuration found in the system-wide "etc" directory
+	 *
 	 * @param parent
 	 *            a config with values not found directly in the returned
 	 *            config. Null is a reasonable value here.
@@ -235,11 +251,15 @@ public abstract class SystemReader {
 	public abstract FileBasedConfig openSystemConfig(Config parent, FS fs);
 
 	/**
+	 * Get the current system time
+	 *
 	 * @return the current system time
 	 */
 	public abstract long getCurrentTime();
 
 	/**
+	 * Get clock instance preferred by this system.
+	 *
 	 * @return clock instance preferred by this system.
 	 * @since 4.6
 	 */
@@ -248,12 +268,17 @@ public abstract class SystemReader {
 	}
 
 	/**
-	 * @param when TODO
+	 * Get the local time zone
+	 *
+	 * @param when
+	 *            a system timestamp
 	 * @return the local time zone
 	 */
 	public abstract int getTimezone(long when);
 
 	/**
+	 * Get system time zone, possibly mocked for testing
+	 *
 	 * @return system time zone, possibly mocked for testing
 	 * @since 1.2
 	 */
@@ -262,6 +287,8 @@ public abstract class SystemReader {
 	}
 
 	/**
+	 * Get the locale to use
+	 *
 	 * @return the locale to use
 	 * @since 1.2
 	 */
@@ -274,7 +301,7 @@ public abstract class SystemReader {
 	 *
 	 * @param pattern
 	 *            the pattern as defined in
-	 *            {@link SimpleDateFormat#SimpleDateFormat(String)}
+	 *            {@link java.text.SimpleDateFormat#SimpleDateFormat(String)}
 	 * @return the simple date format
 	 * @since 2.0
 	 */
@@ -287,7 +314,7 @@ public abstract class SystemReader {
 	 *
 	 * @param pattern
 	 *            the pattern as defined in
-	 *            {@link SimpleDateFormat#SimpleDateFormat(String)}
+	 *            {@link java.text.SimpleDateFormat#SimpleDateFormat(String)}
 	 * @param locale
 	 *            locale to be used for the {@code SimpleDateFormat}
 	 * @return the simple date format
@@ -302,10 +329,10 @@ public abstract class SystemReader {
 	 *
 	 * @param dateStyle
 	 *            the date style as specified in
-	 *            {@link DateFormat#getDateTimeInstance(int, int)}
+	 *            {@link java.text.DateFormat#getDateTimeInstance(int, int)}
 	 * @param timeStyle
 	 *            the time style as specified in
-	 *            {@link DateFormat#getDateTimeInstance(int, int)}
+	 *            {@link java.text.DateFormat#getDateTimeInstance(int, int)}
 	 * @return the date format
 	 * @since 2.0
 	 */
@@ -314,7 +341,9 @@ public abstract class SystemReader {
 	}
 
 	/**
-	 * @return true if we are running on a Windows.
+	 * Whether we are running on Windows.
+	 *
+	 * @return true if we are running on Windows.
 	 */
 	public boolean isWindows() {
 		if (isWindows == null) {
@@ -325,6 +354,8 @@ public abstract class SystemReader {
 	}
 
 	/**
+	 * Whether we are running on Mac OS X
+	 *
 	 * @return true if we are running on Mac OS X
 	 */
 	public boolean isMacOS() {
@@ -351,7 +382,7 @@ public abstract class SystemReader {
 	 * Scans a multi-directory path string such as {@code "src/main.c"}.
 	 *
 	 * @param path path string to scan.
-	 * @throws CorruptObjectException path is invalid.
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException path is invalid.
 	 * @since 3.6
 	 */
 	public void checkPath(String path) throws CorruptObjectException {
@@ -365,7 +396,7 @@ public abstract class SystemReader {
 	 *
 	 * @param path
 	 *            path string to scan.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             path is invalid.
 	 * @since 4.2
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/util/TemporaryBuffer.java

@@ -114,6 +114,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 		reset();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(final int b) throws IOException {
 		if (overflow != null) {
@@ -134,6 +135,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 		s.buffer[s.count++] = (byte) b;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(final byte[] b, int off, int len) throws IOException {
 		if (overflow == null) {
@@ -162,7 +164,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 	/**
 	 * Dumps the entire buffer into the overflow stream, and flushes it.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the overflow stream cannot be started, or the buffer contents
 	 *             cannot be written to it, or it failed to flush.
 	 */
@@ -177,7 +179,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 *
 	 * @param in
 	 *            the stream to read from, until EOF is reached.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred reading from the input stream, or while
 	 *             writing to a local temporary file.
 	 */
@@ -227,10 +229,8 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 * The buffer is only complete after {@link #close()} has been invoked.
 	 *
 	 * @return the complete byte array; length matches {@link #length()}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred reading from a local temporary file
-	 * @throws OutOfMemoryError
-	 *             the buffer cannot fit in memory
 	 */
 	public byte[] toByteArray() throws IOException {
 		final long len = length();
@@ -253,13 +253,9 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 *
 	 * @param limit
 	 *            the maximum number of bytes to be returned
-	 *
 	 * @return the byte array limited to {@code limit} bytes.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred reading from a local temporary file
-	 * @throws OutOfMemoryError
-	 *             the buffer cannot fit in memory
-	 *
 	 * @since 4.2
 	 */
 	public byte[] toByteArray(int limit) throws IOException {
@@ -288,7 +284,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 *            if not null progress updates are sent here. Caller should
 	 *            initialize the task and the number of work units to <code>
 	 *            {@link #length()}/1024</code>.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred reading from a temporary file on the local
 	 *             system, or writing to the output stream.
 	 */
@@ -310,14 +306,16 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 *
 	 * @return a stream to read from the buffer. The caller must close the
 	 *         stream when it is no longer useful.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred opening the temporary file.
 	 */
 	public InputStream openInputStream() throws IOException {
 		return new BlockInputStream();
 	}
 
-	/** Reset this buffer for reuse, purging all buffered content. */
+	/**
+	 * Reset this buffer for reuse, purging all buffered content.
+	 */
 	public void reset() {
 		if (overflow != null) {
 			destroy();
@@ -334,7 +332,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 	 *
 	 * @return the output stream to receive the buffered content, followed by
 	 *         the remaining output.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the buffer cannot create the overflow stream.
 	 */
 	protected abstract OutputStream overflow() throws IOException;
@@ -363,6 +361,7 @@ public abstract class TemporaryBuffer extends OutputStream {
 		overflow.write(last.buffer, 0, last.count);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		if (overflow != null) {
@@ -374,7 +373,9 @@ public abstract class TemporaryBuffer extends OutputStream {
 		}
 	}
 
-	/** Clear this buffer so it has no data, and cannot be used again. */
+	/**
+	 * Clear this buffer so it has no data, and cannot be used again.
+	 */
 	public void destroy() {
 		blocks = null;
 

org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFInputStream.java

@@ -91,12 +91,14 @@ public class AutoCRLFInputStream extends InputStream {
 		this.detectBinary = detectBinary;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		final int read = read(single, 0, 1);
 		return read == 1 ? single[0] & 0xff : -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] bs, final int off, final int len) throws IOException {
 		if (len == 0)
@@ -135,6 +137,7 @@ public class AutoCRLFInputStream extends InputStream {
 		return n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		in.close();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFOutputStream.java

@@ -75,14 +75,18 @@ public class AutoCRLFOutputStream extends OutputStream {
 	private boolean isBinary;
 
 	/**
-	 * @param out
+	 * <p>Constructor for AutoCRLFOutputStream.</p>
+	 *
+	 * @param out a {@link java.io.OutputStream} object.
 	 */
 	public AutoCRLFOutputStream(OutputStream out) {
 		this(out, true);
 	}
 
 	/**
-	 * @param out
+	 * <p>Constructor for AutoCRLFOutputStream.</p>
+	 *
+	 * @param out a {@link java.io.OutputStream} object.
 	 * @param detectBinary
 	 *            whether binaries should be detected
 	 * @since 4.3
@@ -92,12 +96,14 @@ public class AutoCRLFOutputStream extends OutputStream {
 		this.detectBinary = detectBinary;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) throws IOException {
 		onebytebuf[0] = (byte) b;
 		write(onebytebuf, 0, 1);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b) throws IOException {
 		int overflow = buffer(b, 0, b.length);
@@ -105,6 +111,7 @@ public class AutoCRLFOutputStream extends OutputStream {
 			write(b, b.length - overflow, overflow);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b, final int startOff, final int startLen)
 			throws IOException {
@@ -166,6 +173,7 @@ public class AutoCRLFOutputStream extends OutputStream {
 		write(binbuf, 0, cachedLen);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		if (binbufcnt <= binbuf.length)
@@ -174,6 +182,7 @@ public class AutoCRLFOutputStream extends OutputStream {
 		out.flush();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		flush();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java

@@ -125,12 +125,14 @@ public class AutoLFInputStream extends InputStream {
 		this.abortIfBinary = abortIfBinary;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		final int read = read(single, 0, 1);
 		return read == 1 ? single[0] & 0xff : -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] bs, final int off, final int len)
 			throws IOException {
@@ -171,13 +173,16 @@ public class AutoLFInputStream extends InputStream {
 	}
 
 	/**
-	 * @return true if the stream has detected as a binary so far
+	 * Whether the stream has detected as a binary so far.
+	 *
+	 * @return true if the stream has detected as a binary so far.
 	 * @since 3.3
 	 */
 	public boolean isBinary() {
 		return isBinary;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		in.close();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFOutputStream.java

@@ -76,14 +76,24 @@ public class AutoLFOutputStream extends OutputStream {
 	private boolean isBinary;
 
 	/**
+	 * <p>
+	 * Constructor for AutoLFOutputStream.
+	 * </p>
+	 *
 	 * @param out
+	 *            an {@link java.io.OutputStream} object.
 	 */
 	public AutoLFOutputStream(OutputStream out) {
 		this(out, true);
 	}
 
 	/**
+	 * <p>
+	 * Constructor for AutoLFOutputStream.
+	 * </p>
+	 *
 	 * @param out
+	 *            an {@link java.io.OutputStream} object.
 	 * @param detectBinary
 	 *            whether binaries should be detected
 	 */
@@ -92,12 +102,14 @@ public class AutoLFOutputStream extends OutputStream {
 		this.detectBinary = detectBinary;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) throws IOException {
 		onebytebuf[0] = (byte) b;
 		write(onebytebuf, 0, 1);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b) throws IOException {
 		int overflow = buffer(b, 0, b.length);
@@ -106,6 +118,7 @@ public class AutoLFOutputStream extends OutputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] b, final int startOff, final int startLen)
 			throws IOException {
@@ -180,6 +193,7 @@ public class AutoLFOutputStream extends OutputStream {
 		write(binbuf, 0, cachedLen);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		if (binbufcnt <= binbuf.length) {
@@ -188,6 +202,7 @@ public class AutoLFOutputStream extends OutputStream {
 		out.flush();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		flush();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/CountingOutputStream.java

@@ -46,7 +46,9 @@ package org.eclipse.jgit.util.io;
 import java.io.IOException;
 import java.io.OutputStream;
 
-/** Counts the number of bytes written. */
+/**
+ * Counts the number of bytes written.
+ */
 public class CountingOutputStream extends OutputStream {
 	private final OutputStream out;
 	private long cnt;
@@ -61,28 +63,36 @@ public class CountingOutputStream extends OutputStream {
 		this.out = out;
 	}
 
-	/** @return current number of bytes written. */
+	/**
+	 * Get current number of bytes written.
+	 *
+	 * @return current number of bytes written.
+	 */
 	public long getCount() {
 		return cnt;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int val) throws IOException {
 		out.write(val);
 		cnt++;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] buf, int off, int len) throws IOException {
 		out.write(buf, off, len);
 		cnt += len;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		out.flush();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		out.close();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/DisabledOutputStream.java

@@ -48,7 +48,9 @@ import java.io.OutputStream;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** An OutputStream which always throws IllegalStateExeption during write. */
+/**
+ * An OutputStream which always throws IllegalStateExeption during write.
+ */
 public final class DisabledOutputStream extends OutputStream {
 	/** The canonical instance which always throws IllegalStateException. */
 	public static final DisabledOutputStream INSTANCE = new DisabledOutputStream();
@@ -58,6 +60,7 @@ public final class DisabledOutputStream extends OutputStream {
 		// more than one instance from being created.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) throws IOException {
 		// We shouldn't be writing output at this stage, there

org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolCanonicalizingInputStream.java

@@ -52,7 +52,7 @@ import java.io.InputStream;
  * Optionally, a binary check on the first 8000 bytes is performed and in case
  * of binary files, canonicalization is turned off (for the complete file).
  *
- * @deprecated use {@link AutoLFInputStream} instead
+ * @deprecated use {@link org.eclipse.jgit.util.io.AutoLFInputStream} instead
  */
 @Deprecated
 public class EolCanonicalizingInputStream extends AutoLFInputStream {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java

@@ -46,14 +46,13 @@ import java.io.InputStream;
 import java.io.OutputStream;
 
 import org.eclipse.jgit.attributes.Attributes;
-import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
 import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
 import org.eclipse.jgit.treewalk.WorkingTreeOptions;
 
 /**
  * Utility used to create input and output stream wrappers for
- * {@link EolStreamType}
+ * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
  *
  * @since 4.3
  */
@@ -73,16 +72,21 @@ public final class EolStreamTypeUtil {
 	 * <li>working tree .gitattributes</li>
 	 *
 	 * @param op
-	 *            is the {@link OperationType} of the current traversal
+	 *            is the
+	 *            {@link org.eclipse.jgit.treewalk.TreeWalk.OperationType} of
+	 *            the current traversal
 	 * @param options
-	 *            are the {@link Config} options with key
-	 *            {@link WorkingTreeOptions#KEY}
+	 *            are the {@link org.eclipse.jgit.lib.Config} options with key
+	 *            {@link org.eclipse.jgit.treewalk.WorkingTreeOptions#KEY}
 	 * @param attrs
-	 *            are the {@link Attributes} of the file for which the
-	 *            {@link EolStreamType} is to be detected
-	 *
-	 * @return the stream conversion {@link EolStreamType} to be performed for
-	 *         the selected {@link OperationType}
+	 *            are the {@link org.eclipse.jgit.attributes.Attributes} of the
+	 *            file for which the
+	 *            {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType} is to be
+	 *            detected
+	 * @return the stream conversion
+	 *         {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType} to be
+	 *         performed for the selected
+	 *         {@link org.eclipse.jgit.treewalk.TreeWalk.OperationType}
 	 */
 	public static EolStreamType detectStreamType(OperationType op,
 			WorkingTreeOptions options, Attributes attrs) {
@@ -97,11 +101,15 @@ public final class EolStreamTypeUtil {
 	}
 
 	/**
+	 * Wrap the input stream depending on
+	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
+	 *
 	 * @param in
 	 *            original stream
 	 * @param conversion
 	 *            to be performed
-	 * @return the converted stream depending on {@link EolStreamType}
+	 * @return the converted stream depending on
+	 *         {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
 	 */
 	public static InputStream wrapInputStream(InputStream in,
 			EolStreamType conversion) {
@@ -120,11 +128,15 @@ public final class EolStreamTypeUtil {
 	}
 
 	/**
+	 * Wrap the output stream depending on
+	 * {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
+	 *
 	 * @param out
 	 *            original stream
 	 * @param conversion
 	 *            to be performed
-	 * @return the converted stream depending on {@link EolStreamType}
+	 * @return the converted stream depending on
+	 *         {@link org.eclipse.jgit.lib.CoreConfig.EolStreamType}
 	 */
 	public static OutputStream wrapOutputStream(OutputStream out,
 			EolStreamType conversion) {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/InterruptTimer.java

@@ -88,7 +88,9 @@ public final class InterruptTimer {
 
 	final AutoKiller autoKiller;
 
-	/** Create a new timer with a default thread name. */
+	/**
+	 * Create a new timer with a default thread name.
+	 */
 	public InterruptTimer() {
 		this("JGit-InterruptTimer"); //$NON-NLS-1$
 	}
@@ -123,12 +125,16 @@ public final class InterruptTimer {
 		state.begin(timeout);
 	}
 
-	/** Disable the interrupt timer, as the operation is complete. */
+	/**
+	 * Disable the interrupt timer, as the operation is complete.
+	 */
 	public void end() {
 		state.end();
 	}
 
-	/** Shutdown the timer thread, and wait for it to terminate. */
+	/**
+	 * Shutdown the timer thread, and wait for it to terminate.
+	 */
 	public void terminate() {
 		state.terminate();
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/IsolatedOutputStream.java

@@ -91,11 +91,13 @@ public class IsolatedOutputStream extends OutputStream {
 				new ArrayBlockingQueue<Runnable>(1), new NamedThreadFactory());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int ch) throws IOException {
 		write(new byte[] { (byte) ch }, 0, 1);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(final byte[] buf, final int pos, final int cnt)
 			throws IOException {
@@ -109,6 +111,7 @@ public class IsolatedOutputStream extends OutputStream {
 		});
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		checkClosed();
@@ -121,6 +124,7 @@ public class IsolatedOutputStream extends OutputStream {
 		});
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		if (!copier.isShutdown()) {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/LimitedInputStream.java

@@ -51,13 +51,13 @@ import java.io.InputStream;
 import org.eclipse.jgit.internal.JGitText;
 
 /**
- * Wraps a {@link InputStream}, limiting the number of bytes which can be
- * read.
+ * Wraps a {@link java.io.InputStream}, limiting the number of bytes which can
+ * be read.
  *
- * This class was copied and modifed from the Google Guava 16.0. Differently from
- * the original Guava code, when a caller tries to read from this stream past
- * the given limit and the wrapped stream hasn't yet reached its EOF this class
- * will call the limitExceeded method instead of returning EOF.
+ * This class was copied and modifed from the Google Guava 16.0. Differently
+ * from the original Guava code, when a caller tries to read from this stream
+ * past the given limit and the wrapped stream hasn't yet reached its EOF this
+ * class will call the limitExceeded method instead of returning EOF.
  *
  * @since 3.3
  */
@@ -80,18 +80,21 @@ public abstract class LimitedInputStream extends FilterInputStream {
 		this.limit = limit;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int available() throws IOException {
 		return (int) Math.min(in.available(), left);
 	}
 
 	// it's okay to mark even if mark isn't supported, as reset won't work
+	/** {@inheritDoc} */
 	@Override
 	public synchronized void mark(int readLimit) {
 		in.mark(readLimit);
 		mark = left;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		if (left == 0) {
@@ -107,6 +110,7 @@ public abstract class LimitedInputStream extends FilterInputStream {
 		return result;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] b, int off, int len) throws IOException {
 		if (left == 0) {
@@ -123,6 +127,7 @@ public abstract class LimitedInputStream extends FilterInputStream {
 		return result;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public synchronized void reset() throws IOException {
 		if (!in.markSupported())
@@ -135,6 +140,7 @@ public abstract class LimitedInputStream extends FilterInputStream {
 		left = mark;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long skip(long n) throws IOException {
 		n = Math.min(n, left);
@@ -147,10 +153,11 @@ public abstract class LimitedInputStream extends FilterInputStream {
 	 * Called when trying to read past the given {@link #limit} and the wrapped
 	 * InputStream {@link #in} hasn't yet reached its EOF
 	 *
-	 * @throws IOException
-	 *            subclasses can throw an IOException when the limit is exceeded.
-	 *            The throws IOException will be forwarded back to the caller of
-	 *            the read method which read the stream past the limit.
+	 * @throws java.io.IOException
+	 *             subclasses can throw an {@link java.io.IOException} when the
+	 *             limit is exceeded. The throws java.io.IOException will be
+	 *             forwarded back to the caller of the read method which read
+	 *             the stream past the limit.
 	 */
 	protected abstract void limitExceeded() throws IOException;
 }

org.eclipse.jgit/src/org/eclipse/jgit/util/io/MessageWriter.java

@@ -66,20 +66,24 @@ import org.eclipse.jgit.util.RawParseUtils;
  * {@link #toString()} returns all written data, after converting it to a String
  * under the assumption of UTF-8 encoding.
  * <p>
- * Internally {@link RawParseUtils#decode(byte[])} is used by {@code toString()}
- * tries to work out a reasonably correct character set for the raw data.
+ * Internally {@link org.eclipse.jgit.util.RawParseUtils#decode(byte[])} is used
+ * by {@code toString()} tries to work out a reasonably correct character set
+ * for the raw data.
  */
 public class MessageWriter extends Writer {
 	private final ByteArrayOutputStream buf;
 
 	private final OutputStreamWriter enc;
 
-	/** Create an empty writer. */
+	/**
+	 * Create an empty writer.
+	 */
 	public MessageWriter() {
 		buf = new ByteArrayOutputStream();
 		enc = new OutputStreamWriter(getRawStream(), Constants.CHARSET);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(char[] cbuf, int off, int len) throws IOException {
 		synchronized (buf) {
@@ -89,6 +93,9 @@ public class MessageWriter extends Writer {
 	}
 
 	/**
+	 * Get the underlying byte stream that character writes to this writer drop
+	 * into.
+	 *
 	 * @return the underlying byte stream that character writes to this writer
 	 *         drop into. Writes to this stream should should be in UTF-8.
 	 */
@@ -96,17 +103,20 @@ public class MessageWriter extends Writer {
 		return buf;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		// Do nothing, we are buffered with no resources.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		// Do nothing, we are buffered with no resources.
 	}
 
 	/** @return string version of all buffered data. */
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return RawParseUtils.decode(buf.toByteArray());

org.eclipse.jgit/src/org/eclipse/jgit/util/io/NullOutputStream.java

@@ -57,16 +57,19 @@ public class NullOutputStream extends OutputStream {
 		// more than one instance from being created.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) {
 		// Discard.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] buf) {
 		// Discard.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] buf, int pos, int cnt) {
 		// Discard.

org.eclipse.jgit/src/org/eclipse/jgit/util/io/SafeBufferedOutputStream.java

@@ -46,11 +46,15 @@ import java.io.BufferedOutputStream;
 import java.io.OutputStream;
 
 /**
+ * <p>SafeBufferedOutputStream class.</p>
+ *
  * @deprecated use BufferedOutputStream in Java 8 and later.
  */
 @Deprecated
 public class SafeBufferedOutputStream extends BufferedOutputStream {
 	/**
+	 * <p>Constructor for SafeBufferedOutputStream.</p>
+	 *
 	 * @see BufferedOutputStream#BufferedOutputStream(OutputStream)
 	 * @param out
 	 *            underlying output stream
@@ -60,6 +64,8 @@ public class SafeBufferedOutputStream extends BufferedOutputStream {
 	}
 
 	/**
+	 * <p>Constructor for SafeBufferedOutputStream.</p>
+	 *
 	 * @see BufferedOutputStream#BufferedOutputStream(OutputStream, int)
 	 * @param out
 	 *            underlying output stream

org.eclipse.jgit/src/org/eclipse/jgit/util/io/StreamCopyThread.java

@@ -48,7 +48,9 @@ import java.io.InputStream;
 import java.io.InterruptedIOException;
 import java.io.OutputStream;
 
-/** Thread to copy from an input stream to an output stream. */
+/**
+ * Thread to copy from an input stream to an output stream.
+ */
 public class StreamCopyThread extends Thread {
 	private static final int BUFFER_SIZE = 1024;
 
@@ -98,7 +100,7 @@ public class StreamCopyThread extends Thread {
 	 * This method signals to the copy thread that it should stop as soon as
 	 * there is no more IO occurring.
 	 *
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             the calling thread was interrupted.
 	 */
 	public void halt() throws InterruptedException {
@@ -112,6 +114,7 @@ public class StreamCopyThread extends Thread {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void run() {
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/TeeInputStream.java

@@ -47,15 +47,13 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-import org.eclipse.jgit.util.TemporaryBuffer;
-
 /**
  * Input stream that copies data read to another output stream.
  *
- * This stream is primarily useful with a {@link TemporaryBuffer}, where any
- * data read or skipped by the caller is also duplicated into the temporary
- * buffer. Later the temporary buffer can then be used instead of the original
- * source stream.
+ * This stream is primarily useful with a
+ * {@link org.eclipse.jgit.util.TemporaryBuffer}, where any data read or skipped
+ * by the caller is also duplicated into the temporary buffer. Later the
+ * temporary buffer can then be used instead of the original source stream.
  *
  * During close this stream copies any remaining data from the source stream
  * into the destination stream.
@@ -74,13 +72,14 @@ public class TeeInputStream extends InputStream {
 	 *            source stream to consume.
 	 * @param dst
 	 *            destination to copy the source to as it is consumed. Typically
-	 *            this is a {@link TemporaryBuffer}.
+	 *            this is a {@link org.eclipse.jgit.util.TemporaryBuffer}.
 	 */
 	public TeeInputStream(InputStream src, OutputStream dst) {
 		this.src = src;
 		this.dst = dst;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		byte[] b = skipBuffer();
@@ -88,6 +87,7 @@ public class TeeInputStream extends InputStream {
 		return n == 1 ? b[0] & 0xff : -1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long skip(final long count) throws IOException {
 		long skipped = 0;
@@ -104,6 +104,7 @@ public class TeeInputStream extends InputStream {
 		return skipped;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] b, int off, int len) throws IOException {
 		if (len == 0)
@@ -115,6 +116,7 @@ public class TeeInputStream extends InputStream {
 		return n;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		byte[] b = skipBuffer();

org.eclipse.jgit/src/org/eclipse/jgit/util/io/ThrowingPrintWriter.java

@@ -64,7 +64,7 @@ public class ThrowingPrintWriter extends Writer {
 	 * Construct a JGitPrintWriter
 	 *
 	 * @param out
-	 *            the underlying {@link Writer}
+	 *            the underlying {@link java.io.Writer}
 	 */
 	public ThrowingPrintWriter(Writer out) {
 		this.out = out;
@@ -76,16 +76,19 @@ public class ThrowingPrintWriter extends Writer {
 		});
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(char[] cbuf, int off, int len) throws IOException {
 		out.write(cbuf, off, len);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		out.flush();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		out.close();
@@ -94,8 +97,8 @@ public class ThrowingPrintWriter extends Writer {
 	/**
 	 * Print a string and terminate with a line feed.
 	 *
-	 * @param s
-	 * @throws IOException
+	 * @param s a {@link java.lang.String} object.
+	 * @throws java.io.IOException
 	 */
 	public void println(String s) throws IOException {
 		print(s + LF);
@@ -104,7 +107,7 @@ public class ThrowingPrintWriter extends Writer {
 	/**
 	 * Print a platform dependent new line
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void println() throws IOException {
 		print(LF);
@@ -113,8 +116,8 @@ public class ThrowingPrintWriter extends Writer {
 	/**
 	 * Print a char
 	 *
-	 * @param value
-	 * @throws IOException
+	 * @param value a char.
+	 * @throws java.io.IOException
 	 */
 	public void print(char value) throws IOException {
 		print(String.valueOf(value));
@@ -124,7 +127,8 @@ public class ThrowingPrintWriter extends Writer {
 	 * Print an int as string
 	 *
 	 * @param value
-	 * @throws IOException
+	 *            an int.
+	 * @throws java.io.IOException
 	 */
 	public void print(int value) throws IOException {
 		print(String.valueOf(value));
@@ -133,8 +137,8 @@ public class ThrowingPrintWriter extends Writer {
 	/**
 	 * Print a long as string
 	 *
-	 * @param value
-	 * @throws IOException
+	 * @param value a long.
+	 * @throws java.io.IOException
 	 */
 	public void print(long value) throws IOException {
 		print(String.valueOf(value));
@@ -143,8 +147,8 @@ public class ThrowingPrintWriter extends Writer {
 	/**
 	 * Print a short as string
 	 *
-	 * @param value
-	 * @throws IOException
+	 * @param value a short.
+	 * @throws java.io.IOException
 	 */
 	public void print(short value) throws IOException {
 		print(String.valueOf(value));
@@ -152,11 +156,13 @@ public class ThrowingPrintWriter extends Writer {
 
 	/**
 	 * Print a formatted message according to
-	 * {@link String#format(String, Object...)}.
+	 * {@link java.lang.String#format(String, Object...)}.
 	 *
 	 * @param fmt
+	 *            a {@link java.lang.String} object.
 	 * @param args
-	 * @throws IOException
+	 *            objects.
+	 * @throws java.io.IOException
 	 */
 	public void format(String fmt, Object... args) throws IOException {
 		print(String.format(fmt, args));
@@ -166,7 +172,8 @@ public class ThrowingPrintWriter extends Writer {
 	 * Print an object's toString representations
 	 *
 	 * @param any
-	 * @throws IOException
+	 *            an object.
+	 * @throws java.io.IOException
 	 */
 	public void print(Object any) throws IOException {
 		out.write(String.valueOf(any));

org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutInputStream.java

@@ -51,7 +51,9 @@ import java.text.MessageFormat;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** InputStream with a configurable timeout. */
+/**
+ * InputStream with a configurable timeout.
+ */
 public class TimeoutInputStream extends FilterInputStream {
 	private final InterruptTimer myTimer;
 
@@ -72,12 +74,18 @@ public class TimeoutInputStream extends FilterInputStream {
 		myTimer = timer;
 	}
 
-	/** @return number of milliseconds before aborting a read. */
+	/**
+	 * Get number of milliseconds before aborting a read.
+	 *
+	 * @return number of milliseconds before aborting a read.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
 
 	/**
+	 * Set number of milliseconds before aborting a read.
+	 *
 	 * @param millis
 	 *            number of milliseconds before aborting a read. Must be > 0.
 	 */
@@ -88,6 +96,7 @@ public class TimeoutInputStream extends FilterInputStream {
 		timeout = millis;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		try {
@@ -100,11 +109,13 @@ public class TimeoutInputStream extends FilterInputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] buf) throws IOException {
 		return read(buf, 0, buf.length);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] buf, int off, int cnt) throws IOException {
 		try {
@@ -117,6 +128,7 @@ public class TimeoutInputStream extends FilterInputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long skip(long cnt) throws IOException {
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/TimeoutOutputStream.java

@@ -50,7 +50,9 @@ import java.text.MessageFormat;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** OutputStream with a configurable timeout. */
+/**
+ * OutputStream with a configurable timeout.
+ */
 public class TimeoutOutputStream extends OutputStream {
 	private final OutputStream dst;
 
@@ -73,14 +75,21 @@ public class TimeoutOutputStream extends OutputStream {
 		myTimer = timer;
 	}
 
-	/** @return number of milliseconds before aborting a write. */
+	/**
+	 * Get number of milliseconds before aborting a write.
+	 *
+	 * @return number of milliseconds before aborting a write.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
 
 	/**
+	 * Set number of milliseconds before aborting a write.
+	 *
 	 * @param millis
-	 *            number of milliseconds before aborting a write. Must be > 0.
+	 *            number of milliseconds before aborting a write. Must be >
+	 *            0.
 	 */
 	public void setTimeout(final int millis) {
 		if (millis < 0)
@@ -89,6 +98,7 @@ public class TimeoutOutputStream extends OutputStream {
 		timeout = millis;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(int b) throws IOException {
 		try {
@@ -101,11 +111,13 @@ public class TimeoutOutputStream extends OutputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] buf) throws IOException {
 		write(buf, 0, buf.length);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(byte[] buf, int off, int len) throws IOException {
 		try {
@@ -118,6 +130,7 @@ public class TimeoutOutputStream extends OutputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		try {
@@ -130,6 +143,7 @@ public class TimeoutOutputStream extends OutputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/util/io/UnionInputStream.java

@@ -58,7 +58,7 @@ import java.util.LinkedList;
  * Currently this stream does not support the mark/reset APIs. If mark and later
  * reset functionality is needed the caller should wrap this stream with a
  * {@link java.io.BufferedInputStream}.
- * */
+ */
 public class UnionInputStream extends InputStream {
 	private static final InputStream EOF = new InputStream() {
 		@Override
@@ -69,7 +69,9 @@ public class UnionInputStream extends InputStream {
 
 	private final LinkedList<InputStream> streams = new LinkedList<>();
 
-	/** Create an empty InputStream that is currently at EOF state. */
+	/**
+	 * Create an empty InputStream that is currently at EOF state.
+	 */
 	public UnionInputStream() {
 		// Do nothing.
 	}
@@ -122,6 +124,7 @@ public class UnionInputStream extends InputStream {
 		return streams.isEmpty();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		for (;;) {
@@ -136,6 +139,7 @@ public class UnionInputStream extends InputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(byte[] b, int off, int len) throws IOException {
 		if (len == 0)
@@ -152,11 +156,13 @@ public class UnionInputStream extends InputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int available() throws IOException {
 		return head().available();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long skip(final long count) throws IOException {
 		long skipped = 0;
@@ -190,6 +196,7 @@ public class UnionInputStream extends InputStream {
 		return skipped;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() throws IOException {
 		IOException err = null;

org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/SHA1.java

@@ -70,8 +70,8 @@ import org.slf4j.LoggerFactory;
  * sha1collisiondetection</a> for more information.
  * <p>
  * When detectCollision is true (default), this implementation throws
- * {@link Sha1CollisionException} from any digest method if a potential
- * collision was detected.
+ * {@link org.eclipse.jgit.util.sha1.Sha1CollisionException} from any digest
+ * method if a potential collision was detected.
  *
  * @since 4.7
  */
@@ -85,7 +85,11 @@ public class SHA1 {
 		DETECT_COLLISIONS = v != null ? Boolean.parseBoolean(v) : true;
 	}
 
-	/** @return a new context to compute a SHA-1 hash of data. */
+	/**
+	 * Create a new context to compute a SHA-1 hash of data.
+	 *
+	 * @return a new context to compute a SHA-1 hash of data.
+	 */
 	public static SHA1 newInstance() {
 		return new SHA1();
 	}
@@ -121,6 +125,7 @@ public class SHA1 {
 	 * {@code -Dorg.eclipse.jgit.util.sha1.detectCollision=true}.
 	 *
 	 * @param detect
+	 *            a boolean.
 	 * @return {@code this}
 	 */
 	public SHA1 setDetectCollision(boolean detect) {
@@ -131,7 +136,7 @@ public class SHA1 {
 	/**
 	 * Update the digest computation by adding a byte.
 	 *
-	 * @param b
+	 * @param b a byte.
 	 */
 	public void update(byte b) {
 		int bufferLen = (int) (length & 63);
@@ -503,7 +508,7 @@ public class SHA1 {
 	 * Once {@code digest()} is called, this instance should be discarded.
 	 *
 	 * @return the bytes for the resulting hash.
-	 * @throws Sha1CollisionException
+	 * @throws org.eclipse.jgit.util.sha1.Sha1CollisionException
 	 *             if a collision was detected and safeHash is false.
 	 */
 	public byte[] digest() throws Sha1CollisionException {
@@ -524,7 +529,7 @@ public class SHA1 {
 	 * Once {@code digest()} is called, this instance should be discarded.
 	 *
 	 * @return the ObjectId for the resulting hash.
-	 * @throws Sha1CollisionException
+	 * @throws org.eclipse.jgit.util.sha1.Sha1CollisionException
 	 *             if a collision was detected and safeHash is false.
 	 */
 	public ObjectId toObjectId() throws Sha1CollisionException {
@@ -539,7 +544,7 @@ public class SHA1 {
 	 *
 	 * @param id
 	 *            destination to copy the digest to.
-	 * @throws Sha1CollisionException
+	 * @throws org.eclipse.jgit.util.sha1.Sha1CollisionException
 	 *             if a collision was detected and safeHash is false.
 	 */
 	public void digest(MutableObjectId id) throws Sha1CollisionException {

org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/Sha1CollisionException.java

@@ -49,7 +49,8 @@ import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.ObjectId;
 
 /**
- * Thrown by {@link SHA1} if it detects a likely hash collision.
+ * Thrown by {@link org.eclipse.jgit.util.sha1.SHA1} if it detects a likely hash
+ * collision.
  *
  * @since 4.7
  */

org.eclipse.jgit/src/org/eclipse/jgit/util/time/MonotonicClock.java

@@ -44,7 +44,6 @@
 package org.eclipse.jgit.util.time;
 
 import java.time.Duration;
-import java.util.concurrent.TimeUnit;
 
 /**
  * A provider of time.
@@ -53,7 +52,9 @@ import java.util.concurrent.TimeUnit;
  * source, such as the local system clock.
  * <p>
  * MonotonicClocks provide the following behavior, with the assertion always
- * being true if {@link ProposedTimestamp#blockUntil(Duration)} is used:
+ * being true if
+ * {@link org.eclipse.jgit.util.time.ProposedTimestamp#blockUntil(Duration)} is
+ * used:
  *
  * <pre>
  *   MonotonicClock clk = ...;
@@ -83,14 +84,11 @@ public interface MonotonicClock {
 	 * by NTP) and return that proposal, concurrently sending network messages
 	 * to closely collaborating peers in the same cluster to also ensure their
 	 * system clocks are ahead of this time. In such an implementation the
-	 * {@link ProposedTimestamp#blockUntil(Duration)} method would wait for
-	 * replies from the peers indicating their own system clocks have moved past
-	 * the proposed time.
+	 * {@link org.eclipse.jgit.util.time.ProposedTimestamp#blockUntil(Duration)}
+	 * method would wait for replies from the peers indicating their own system
+	 * clocks have moved past the proposed time.
 	 *
-	 * @return "now". The value can be immediately accessed by
-	 *         {@link ProposedTimestamp#read(TimeUnit)} and friends, but the
-	 *         caller must use {@link ProposedTimestamp#blockUntil(Duration)} to
-	 *         ensure ordering holds.
+	 * @return a {@link org.eclipse.jgit.util.time.ProposedTimestamp} object.
 	 */
 	ProposedTimestamp propose();
 }

org.eclipse.jgit/src/org/eclipse/jgit/util/time/MonotonicSystemClock.java

@@ -51,7 +51,8 @@ import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicLong;
 
 /**
- * A {@link MonotonicClock} based on {@code System.currentTimeMillis}.
+ * A {@link org.eclipse.jgit.util.time.MonotonicClock} based on
+ * {@code System.currentTimeMillis}.
  *
  * @since 4.6
  */
@@ -69,6 +70,7 @@ public class MonotonicSystemClock implements MonotonicClock {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ProposedTimestamp propose() {
 		final long u = nowMicros();

org.eclipse.jgit/src/org/eclipse/jgit/util/time/ProposedTimestamp.java

@@ -55,7 +55,8 @@ import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
 
 /**
- * A timestamp generated by {@link MonotonicClock#propose()}.
+ * A timestamp generated by
+ * {@link org.eclipse.jgit.util.time.MonotonicClock#propose()}.
  * <p>
  * ProposedTimestamp implements AutoCloseable so that implementations can
  * release resources associated with obtaining certainty about time elapsing.
@@ -73,10 +74,10 @@ public abstract class ProposedTimestamp implements AutoCloseable {
 	 *            timestamps to wait on.
 	 * @param maxWait
 	 *            how long to wait for the timestamps.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             current thread was interrupted before the waiting process
 	 *             completed normally.
-	 * @throws TimeoutException
+	 * @throws java.util.concurrent.TimeoutException
 	 *             the timeout was reached without the proposed timestamp become
 	 *             certainly in the past.
 	 */
@@ -121,31 +122,44 @@ public abstract class ProposedTimestamp implements AutoCloseable {
 	 * <p>
 	 * This method forces the caller to wait up to {@code timeout} for
 	 * {@code this} to pass sufficiently into the past such that the creating
-	 * {@link MonotonicClock} instance will not create an earlier timestamp.
+	 * {@link org.eclipse.jgit.util.time.MonotonicClock} instance will not
+	 * create an earlier timestamp.
 	 *
 	 * @param maxWait
 	 *            how long the implementation may block the caller.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             current thread was interrupted before the waiting process
 	 *             completed normally.
-	 * @throws TimeoutException
+	 * @throws java.util.concurrent.TimeoutException
 	 *             the timeout was reached without the proposed timestamp
 	 *             becoming certainly in the past.
 	 */
 	public abstract void blockUntil(Duration maxWait)
 			throws InterruptedException, TimeoutException;
 
-	/** @return milliseconds since epoch; {@code read(MILLISECONDS}). */
+	/**
+	 * Get milliseconds since epoch; {@code read(MILLISECONDS}).
+	 *
+	 * @return milliseconds since epoch; {@code read(MILLISECONDS}).
+	 */
 	public long millis() {
 		return read(MILLISECONDS);
 	}
 
-	/** @return microseconds since epoch; {@code read(MICROSECONDS}). */
+	/**
+	 * Get microseconds since epoch; {@code read(MICROSECONDS}).
+	 *
+	 * @return microseconds since epoch; {@code read(MICROSECONDS}).
+	 */
 	public long micros() {
 		return read(MICROSECONDS);
 	}
 
-	/** @return time since epoch, with up to microsecond resolution. */
+	/**
+	 * Get time since epoch, with up to microsecond resolution.
+	 *
+	 * @return time since epoch, with up to microsecond resolution.
+	 */
 	public Instant instant() {
 		long usec = micros();
 		long secs = usec / 1000000L;
@@ -153,22 +167,35 @@ public abstract class ProposedTimestamp implements AutoCloseable {
 		return Instant.ofEpochSecond(secs, nanos);
 	}
 
-	/** @return time since epoch, with up to microsecond resolution. */
+	/**
+	 * Get time since epoch, with up to microsecond resolution.
+	 *
+	 * @return time since epoch, with up to microsecond resolution.
+	 */
 	public Timestamp timestamp() {
 		return Timestamp.from(instant());
 	}
 
-	/** @return time since epoch, with up to millisecond resolution. */
+	/**
+	 * Get time since epoch, with up to millisecond resolution.
+	 *
+	 * @return time since epoch, with up to millisecond resolution.
+	 */
 	public Date date() {
 		return new Date(millis());
 	}
 
-	/** Release resources allocated by this timestamp. */
+	/**
+	 * {@inheritDoc}
+	 * <p>
+	 * Release resources allocated by this timestamp.
+	 */
 	@Override
 	public void close() {
 		// Do nothing by default.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return instant().toString();