Fix javadoc in org.eclipse.jgit lib package

Change-Id: I1e85a951488177993521ce177fdea212615e6164
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java

@@ -52,7 +52,7 @@ import org.eclipse.jgit.util.NB;
 import org.eclipse.jgit.util.RawParseUtils;
 
 /**
- * A prefix abbreviation of an {@link ObjectId}.
+ * A prefix abbreviation of an {@link org.eclipse.jgit.lib.ObjectId}.
  * <p>
  * Sometimes Git produces abbreviated SHA-1 strings, using sufficient leading
  * digits from the ObjectId name to still be unique within the repository the
@@ -109,13 +109,14 @@ public final class AbbreviatedObjectId implements Serializable {
 	}
 
 	/**
-	 * Convert an AbbreviatedObjectId from an {@link AnyObjectId}.
+	 * Convert an AbbreviatedObjectId from an
+	 * {@link org.eclipse.jgit.lib.AnyObjectId}.
 	 * <p>
 	 * This method copies over all bits of the Id, and is therefore complete
 	 * (see {@link #isComplete()}).
 	 *
 	 * @param id
-	 *            the {@link ObjectId} to convert from.
+	 *            the {@link org.eclipse.jgit.lib.ObjectId} to convert from.
 	 * @return the converted object id.
 	 */
 	public static final AbbreviatedObjectId fromObjectId(AnyObjectId id) {
@@ -205,17 +206,29 @@ public final class AbbreviatedObjectId implements Serializable {
 		w5 = new_5;
 	}
 
-	/** @return number of hex digits appearing in this id */
+	/**
+	 * Get number of hex digits appearing in this id.
+	 *
+	 * @return number of hex digits appearing in this id.
+	 */
 	public int length() {
 		return nibbles;
 	}
 
-	/** @return true if this ObjectId is actually a complete id. */
+	/**
+	 * Whether this ObjectId is actually a complete id.
+	 *
+	 * @return true if this ObjectId is actually a complete id.
+	 */
 	public boolean isComplete() {
 		return length() == Constants.OBJECT_ID_STRING_LENGTH;
 	}
 
-	/** @return a complete ObjectId; null if {@link #isComplete()} is false */
+	/**
+	 * A complete ObjectId; null if {@link #isComplete()} is false
+	 *
+	 * @return a complete ObjectId; null if {@link #isComplete()} is false
+	 */
 	public ObjectId toObjectId() {
 		return isComplete() ? new ObjectId(w1, w2, w3, w4, w5) : null;
 	}
@@ -325,7 +338,11 @@ public final class AbbreviatedObjectId implements Serializable {
 		return NB.compareUInt32(w5, mask(5, bs[p + 4]));
 	}
 
-	/** @return value for a fan-out style map, only valid of length &gt;= 2. */
+	/**
+	 * Get value for a fan-out style map, only valid of length &gt;= 2.
+	 *
+	 * @return value for a fan-out style map, only valid of length &gt;= 2.
+	 */
 	public final int getFirstByte() {
 		return w1 >>> 24;
 	}
@@ -334,11 +351,13 @@ public final class AbbreviatedObjectId implements Serializable {
 		return mask(nibbles, word, v);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		return w1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(final Object o) {
 		if (o instanceof AbbreviatedObjectId) {
@@ -350,6 +369,8 @@ public final class AbbreviatedObjectId implements Serializable {
 	}
 
 	/**
+	 * Get string form of the abbreviation, in lower case hexadecimal.
+	 *
 	 * @return string form of the abbreviation, in lower case hexadecimal.
 	 */
 	public final String name() {
@@ -375,6 +396,7 @@ public final class AbbreviatedObjectId implements Serializable {
 		return new String(b, 0, nibbles);
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java

@@ -53,9 +53,9 @@ import org.eclipse.jgit.util.NB;
 /**
  * A (possibly mutable) SHA-1 abstraction.
  * <p>
- * If this is an instance of {@link MutableObjectId} the concept of equality
- * with this instance can alter at any time, if this instance is modified to
- * represent a different object name.
+ * If this is an instance of {@link org.eclipse.jgit.lib.MutableObjectId} the
+ * concept of equality with this instance can alter at any time, if this
+ * instance is modified to represent a different object name.
  */
 public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 
@@ -117,14 +117,16 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *
 	 * @param index
 	 *            index of the byte to obtain from the raw form of the ObjectId.
-	 *            Must be in range [0, {@link Constants#OBJECT_ID_LENGTH}).
+	 *            Must be in range [0,
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}).
 	 * @return the value of the requested byte at {@code index}. Returned values
 	 *         are unsigned and thus are in the range [0,255] rather than the
 	 *         signed byte range of [-128, 127].
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             {@code index} is less than 0, equal to
-	 *             {@link Constants#OBJECT_ID_LENGTH}, or greater than
-	 *             {@link Constants#OBJECT_ID_LENGTH}.
+	 *             {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}, or
+	 *             greater than
+	 *             {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}.
 	 */
 	public final int getByte(int index) {
 		int w;
@@ -152,12 +154,9 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Compare this ObjectId to another and obtain a sort ordering.
-	 *
-	 * @param other
-	 *            the other id to compare to. Must not be null.
-	 * @return &lt; 0 if this id comes before other; 0 if this id is equal to
-	 *         other; &gt; 0 if this id comes after other.
 	 */
 	@Override
 	public final int compareTo(final AnyObjectId other) {
@@ -262,6 +261,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 		return abbr.prefixCompare(this) == 0;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final int hashCode() {
 		return w2;
@@ -278,6 +278,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 		return other != null ? equals(this, other) : false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final boolean equals(final Object o) {
 		if (o instanceof AnyObjectId)
@@ -337,7 +338,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *
 	 * @param w
 	 *            the stream to write to.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream writing failed.
 	 */
 	public void copyRawTo(final OutputStream w) throws IOException {
@@ -361,7 +362,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *
 	 * @param w
 	 *            the stream to copy to.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream writing failed.
 	 */
 	public void copyTo(final OutputStream w) throws IOException {
@@ -422,7 +423,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *
 	 * @param w
 	 *            the stream to copy to.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream writing failed.
 	 */
 	public void copyTo(final Writer w) throws IOException {
@@ -438,7 +439,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *            of object id (40 characters or larger).
 	 * @param w
 	 *            the stream to copy to.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream writing failed.
 	 */
 	public void copyTo(final char[] tmp, final Writer w) throws IOException {
@@ -488,6 +489,7 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 			dst[o--] = '0';
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
@@ -495,6 +497,8 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	}
 
 	/**
+	 * <p>name.</p>
+	 *
 	 * @return string form of the SHA-1, in lower case hexadecimal.
 	 */
 	public final String name() {
@@ -502,6 +506,8 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	}
 
 	/**
+	 * Get string form of the SHA-1, in lower case hexadecimal.
+	 *
 	 * @return string form of the SHA-1, in lower case hexadecimal.
 	 */
 	public final String getName() {
@@ -511,9 +517,11 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	/**
 	 * Return an abbreviation (prefix) of this object SHA-1.
 	 * <p>
-	 * This implementation does not guarantee uniqueness. Callers should
-	 * instead use {@link ObjectReader#abbreviate(AnyObjectId, int)} to obtain a
-	 * unique abbreviation within the scope of a particular object database.
+	 * This implementation does not guarantee uniqueness. Callers should instead
+	 * use
+	 * {@link org.eclipse.jgit.lib.ObjectReader#abbreviate(AnyObjectId, int)} to
+	 * obtain a unique abbreviation within the scope of a particular object
+	 * database.
 	 *
 	 * @param len
 	 *            length of the abbreviated string.
@@ -532,8 +540,8 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 * Obtain an immutable copy of this current object name value.
 	 * <p>
 	 * Only returns <code>this</code> if this instance is an unsubclassed
-	 * instance of {@link ObjectId}; otherwise a new instance is returned
-	 * holding the same value.
+	 * instance of {@link org.eclipse.jgit.lib.ObjectId}; otherwise a new
+	 * instance is returned holding the same value.
 	 * <p>
 	 * This method is useful to shed any additional memory that may be tied to
 	 * the subclass, yet retain the unique identity of the object id for future

org.eclipse.jgit/src/org/eclipse/jgit/lib/AsyncObjectLoaderQueue.java

@@ -63,30 +63,37 @@ public interface AsyncObjectLoaderQueue<T extends ObjectId> extends
 	 * Position this queue onto the next available result.
 	 *
 	 * Even if this method returns true, {@link #open()} may still throw
-	 * {@link MissingObjectException} if the underlying object database was
-	 * concurrently modified and the current object is no longer available.
+	 * {@link org.eclipse.jgit.errors.MissingObjectException} if the underlying
+	 * object database was concurrently modified and the current object is no
+	 * longer available.
 	 *
 	 * @return true if there is a result available; false if the queue has
 	 *         finished its input iteration.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist. If the implementation is retaining
 	 *             the application's objects {@link #getCurrent()} will be the
 	 *             current object that is missing. There may be more results
 	 *             still available, so the caller should continue invoking next
 	 *             to examine another result.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public boolean next() throws MissingObjectException, IOException;
 
 	/**
+	 * Get the current object, null if the implementation lost track.
+	 *
 	 * @return the current object, null if the implementation lost track.
 	 *         Implementations may for performance reasons discard the caller's
 	 *         ObjectId and provider their own through {@link #getObjectId()}.
 	 */
 	public T getCurrent();
 
-	/** @return the ObjectId of the current object. Never null. */
+	/**
+	 * Get the ObjectId of the current object. Never null.
+	 *
+	 * @return the ObjectId of the current object. Never null.
+	 */
 	public ObjectId getObjectId();
 
 	/**
@@ -105,7 +112,7 @@ public interface AsyncObjectLoaderQueue<T extends ObjectId> extends
 	 *             current object that is missing. There may be more results
 	 *             still available, so the caller should continue invoking next
 	 *             to examine another result.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open() throws IOException;

org.eclipse.jgit/src/org/eclipse/jgit/lib/AsyncObjectSizeQueue.java

@@ -64,27 +64,37 @@ public interface AsyncObjectSizeQueue<T extends ObjectId> extends
 	 *
 	 * @return true if there is a result available; false if the queue has
 	 *         finished its input iteration.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist. If the implementation is retaining
 	 *             the application's objects {@link #getCurrent()} will be the
 	 *             current object that is missing. There may be more results
 	 *             still available, so the caller should continue invoking next
 	 *             to examine another result.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public boolean next() throws MissingObjectException, IOException;
 
 	/**
+	 * <p>getCurrent.</p>
+	 *
 	 * @return the current object, null if the implementation lost track.
 	 *         Implementations may for performance reasons discard the caller's
 	 *         ObjectId and provider their own through {@link #getObjectId()}.
 	 */
 	public T getCurrent();
 
-	/** @return the ObjectId of the current object. Never null. */
+	/**
+	 * Get the ObjectId of the current object. Never null.
+	 *
+	 * @return the ObjectId of the current object. Never null.
+	 */
 	public ObjectId getObjectId();
 
-	/** @return the size of the current object. */
+	/**
+	 * Get the size of the current object.
+	 *
+	 * @return the size of the current object.
+	 */
 	public long getSize();
 }

org.eclipse.jgit/src/org/eclipse/jgit/lib/AsyncOperation.java

@@ -70,6 +70,8 @@ public interface AsyncOperation {
 	 */
 	public boolean cancel(boolean mayInterruptIfRunning);
 
-	/** Release resources used by the operation, including cancellation. */
+	/**
+	 * Release resources used by the operation, including cancellation.
+	 */
 	public void release();
 }

org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java

@@ -160,7 +160,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return the file system abstraction, or null if not set. */
+	/**
+	 * Get the file system abstraction, or null if not set.
+	 *
+	 * @return the file system abstraction, or null if not set.
+	 */
 	public FS getFS() {
 		return fs;
 	}
@@ -182,7 +186,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return the meta data directory; null if not set. */
+	/**
+	 * Get the meta data directory; null if not set.
+	 *
+	 * @return the meta data directory; null if not set.
+	 */
 	public File getGitDir() {
 		return gitDir;
 	}
@@ -200,7 +208,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return the object directory; null if not set. */
+	/**
+	 * Get the object directory; null if not set.
+	 *
+	 * @return the object directory; null if not set.
+	 */
 	public File getObjectDirectory() {
 		return objectDirectory;
 	}
@@ -262,7 +274,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return ordered array of alternate directories; null if non were set. */
+	/**
+	 * Get ordered array of alternate directories; null if non were set.
+	 *
+	 * @return ordered array of alternate directories; null if non were set.
+	 */
 	public File[] getAlternateObjectDirectories() {
 		final List<File> alts = alternateObjectDirectories;
 		if (alts == null)
@@ -285,7 +301,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return true if this repository was forced bare by {@link #setBare()}. */
+	/**
+	 * Whether this repository was forced bare by {@link #setBare()}.
+	 *
+	 * @return true if this repository was forced bare by {@link #setBare()}.
+	 */
 	public boolean isBare() {
 		return bare;
 	}
@@ -303,7 +323,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return true if the repository must exist before being opened. */
+	/**
+	 * Whether the repository must exist before being opened.
+	 *
+	 * @return true if the repository must exist before being opened.
+	 */
 	public boolean isMustExist() {
 		return mustExist;
 	}
@@ -320,7 +344,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return the work tree directory, or null if not set. */
+	/**
+	 * Get the work tree directory, or null if not set.
+	 *
+	 * @return the work tree directory, or null if not set.
+	 */
 	public File getWorkTree() {
 		return workTree;
 	}
@@ -341,7 +369,11 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return self();
 	}
 
-	/** @return the index file location, or null if not set. */
+	/**
+	 * Get the index file location, or null if not set.
+	 *
+	 * @return the index file location, or null if not set.
+	 */
 	public File getIndexFile() {
 		return indexFile;
 	}
@@ -544,10 +576,10 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * exception is thrown to the caller.
 	 *
 	 * @return {@code this}
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             insufficient parameters were set, or some parameters are
 	 *             incompatible with one another.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be accessed to configure the rest of
 	 *             the builder's parameters.
 	 */
@@ -569,9 +601,9 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * @return a repository matching this configuration. The caller is
 	 *         responsible to close the repository instance when it is no longer
 	 *         needed.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             insufficient parameters were set.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be accessed to configure the rest of
 	 *             the builder's parameters.
 	 */
@@ -583,7 +615,9 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return repo;
 	}
 
-	/** Require either {@code gitDir} or {@code workTree} to be set. */
+	/**
+	 * Require either {@code gitDir} or {@code workTree} to be set.
+	 */
 	protected void requireGitDirOrWorkTree() {
 		if (getGitDir() == null && getWorkTree() == null)
 			throw new IllegalArgumentException(
@@ -593,7 +627,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	/**
 	 * Perform standard gitDir initialization.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be accessed
 	 */
 	protected void setupGitDir() throws IOException {
@@ -615,7 +649,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * end after the repository has been identified and its configuration is
 	 * available for inspection.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository configuration could not be read.
 	 */
 	protected void setupWorkTree() throws IOException {
@@ -642,7 +676,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	/**
 	 * Configure the internal implementation details of the repository.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be accessed
 	 */
 	protected void setupInternals() throws IOException {
@@ -654,7 +688,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * Get the cached repository configuration, loading if not yet available.
 	 *
 	 * @return the configuration of the repository.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the configuration is not available, or is badly formed.
 	 */
 	protected Config getConfig() throws IOException {
@@ -670,7 +704,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * empty configuration if gitDir was not set.
 	 *
 	 * @return the repository's configuration.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the configuration is not available.
 	 */
 	protected Config loadConfig() throws IOException {
@@ -728,12 +762,20 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		return null;
 	}
 
-	/** @return the configured FS, or {@link FS#DETECTED}. */
+	/**
+	 * Get the configured FS, or {@link FS#DETECTED}.
+	 *
+	 * @return the configured FS, or {@link FS#DETECTED}.
+	 */
 	protected FS safeFS() {
 		return getFS() != null ? getFS() : FS.DETECTED;
 	}
 
-	/** @return {@code this} */
+	/**
+	 * Get this object
+	 *
+	 * @return {@code this}
+	 */
 	@SuppressWarnings("unchecked")
 	protected final B self() {
 		return (B) this;

org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchRefUpdate.java

@@ -135,6 +135,9 @@ public class BatchRefUpdate {
 	}
 
 	/**
+	 * Whether the batch update will permit a non-fast-forward update to an
+	 * existing reference.
+	 *
 	 * @return true if the batch update will permit a non-fast-forward update to
 	 *         an existing reference.
 	 */
@@ -154,7 +157,11 @@ public class BatchRefUpdate {
 		return this;
 	}
 
-	/** @return identity of the user making the change in the reflog. */
+	/**
+	 * Get identity of the user making the change in the reflog.
+	 *
+	 * @return identity of the user making the change in the reflog.
+	 */
 	public PersonIdent getRefLogIdent() {
 		return refLogIdent;
 	}
@@ -193,7 +200,8 @@ public class BatchRefUpdate {
 	 * such as fast-forward or force-update.
 	 * <p>
 	 * Describes the default for commands in this batch that do not override it
-	 * with {@link ReceiveCommand#setRefLogMessage(String, boolean)}.
+	 * with
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand#setRefLogMessage(String, boolean)}.
 	 *
 	 * @return true if the message should include the result.
 	 */
@@ -204,21 +212,23 @@ public class BatchRefUpdate {
 	/**
 	 * Set the message to include in the reflog.
 	 * <p>
-	 * Repository implementations may limit which reflogs are written by default,
-	 * based on the project configuration. If a repo is not configured to write
-	 * logs for this ref by default, setting the message alone may have no effect.
-	 * To indicate that the repo should write logs for this update in spite of
-	 * configured defaults, use {@link #setForceRefLog(boolean)}.
+	 * Repository implementations may limit which reflogs are written by
+	 * default, based on the project configuration. If a repo is not configured
+	 * to write logs for this ref by default, setting the message alone may have
+	 * no effect. To indicate that the repo should write logs for this update in
+	 * spite of configured defaults, use {@link #setForceRefLog(boolean)}.
 	 * <p>
 	 * Describes the default for commands in this batch that do not override it
-	 * with {@link ReceiveCommand#setRefLogMessage(String, boolean)}.
+	 * with
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand#setRefLogMessage(String, boolean)}.
 	 *
 	 * @param msg
-	 *            the message to describe this change. If null and appendStatus is
-	 *            false, the reflog will not be updated.
+	 *            the message to describe this change. If null and appendStatus
+	 *            is false, the reflog will not be updated.
 	 * @param appendStatus
 	 *            true if the status of the ref change (fast-forward or
-	 *            forced-update) should be appended to the user supplied message.
+	 *            forced-update) should be appended to the user supplied
+	 *            message.
 	 * @return {@code this}.
 	 */
 	public BatchRefUpdate setRefLogMessage(String msg, boolean appendStatus) {
@@ -286,12 +296,15 @@ public class BatchRefUpdate {
 	 * {@code REJECTED_OTHER_REASON}.
 	 * <p>
 	 * This method only works if the underlying ref database supports atomic
-	 * transactions, i.e. {@link RefDatabase#performsAtomicTransactions()} returns
-	 * true. Calling this method with true if the underlying ref database does not
-	 * support atomic transactions will cause all commands to fail with {@code
+	 * transactions, i.e.
+	 * {@link org.eclipse.jgit.lib.RefDatabase#performsAtomicTransactions()}
+	 * returns true. Calling this method with true if the underlying ref
+	 * database does not support atomic transactions will cause all commands to
+	 * fail with {@code
 	 * REJECTED_OTHER_REASON}.
 	 *
-	 * @param atomic whether updates should be atomic.
+	 * @param atomic
+	 *            whether updates should be atomic.
 	 * @return {@code this}
 	 * @since 4.4
 	 */
@@ -301,6 +314,8 @@ public class BatchRefUpdate {
 	}
 
 	/**
+	 * Whether updates should be atomic.
+	 *
 	 * @return atomic whether updates should be atomic.
 	 * @since 4.4
 	 */
@@ -335,7 +350,11 @@ public class BatchRefUpdate {
 		return pushCert;
 	}
 
-	/** @return commands this update will process. */
+	/**
+	 * Get commands this update will process.
+	 *
+	 * @return commands this update will process.
+	 */
 	public List<ReceiveCommand> getCommands() {
 		return Collections.unmodifiableList(commands);
 	}
@@ -401,6 +420,8 @@ public class BatchRefUpdate {
 	}
 
 	/**
+	 * Get list of timestamps the batch must wait for.
+	 *
 	 * @return list of timestamps the batch must wait for.
 	 * @since 4.6
 	 */
@@ -415,6 +436,7 @@ public class BatchRefUpdate {
 	 * Request the batch to wait for the affected timestamps to resolve.
 	 *
 	 * @param ts
+	 *            a {@link org.eclipse.jgit.util.time.ProposedTimestamp} object.
 	 * @return {@code this}.
 	 * @since 4.6
 	 */
@@ -434,7 +456,7 @@ public class BatchRefUpdate {
 	 * <p>
 	 * Implementations must respect the atomicity requirements of the underlying
 	 * database as described in {@link #setAtomic(boolean)} and
-	 * {@link RefDatabase#performsAtomicTransactions()}.
+	 * {@link org.eclipse.jgit.lib.RefDatabase#performsAtomicTransactions()}.
 	 *
 	 * @param walk
 	 *            a RevWalk to parse tags in case the storage system wants to
@@ -443,7 +465,7 @@ public class BatchRefUpdate {
 	 *            progress monitor to receive update status on.
 	 * @param options
 	 *            a list of option strings; set null to execute without
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database is unable to accept the update. Individual
 	 *             command status must be tested to determine if there is a
 	 *             partial failure, or a total failure.
@@ -601,7 +623,7 @@ public class BatchRefUpdate {
 	 *            store them pre-peeled, a common performance optimization.
 	 * @param monitor
 	 *            progress monitor to receive update status on.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database is unable to accept the update. Individual
 	 *             command status must be tested to determine if there is a
 	 *             partial failure, or a total failure.
@@ -658,7 +680,7 @@ public class BatchRefUpdate {
 	 * @param cmd
 	 *            specific command the update should be created to copy.
 	 * @return a single reference update command.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference database cannot make a new update object for
 	 *             the given reference.
 	 */
@@ -746,6 +768,7 @@ public class BatchRefUpdate {
 				: isForceRefLog();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		StringBuilder r = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchingProgressMonitor.java

@@ -48,7 +48,9 @@ import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.lib.internal.WorkQueue;
 
-/** ProgressMonitor that batches update events. */
+/**
+ * ProgressMonitor that batches update events.
+ */
 public abstract class BatchingProgressMonitor implements ProgressMonitor {
 	private long delayStartTime;
 
@@ -70,11 +72,13 @@ public abstract class BatchingProgressMonitor implements ProgressMonitor {
 		delayStartUnit = unit;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void start(int totalTasks) {
 		// Ignore the number of tasks.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void beginTask(String title, int work) {
 		endTask();
@@ -83,12 +87,14 @@ public abstract class BatchingProgressMonitor implements ProgressMonitor {
 			task.delay(delayStartTime, delayStartUnit);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void update(int completed) {
 		if (task != null)
 			task.update(this, completed);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void endTask() {
 		if (task != null) {
@@ -97,6 +103,7 @@ public abstract class BatchingProgressMonitor implements ProgressMonitor {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCancelled() {
 		return false;

org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapIndex.java

@@ -63,7 +63,11 @@ public interface BitmapIndex {
 	 */
 	Bitmap getBitmap(AnyObjectId objectId);
 
-	/** @return a new {@code BitmapBuilder} based on the values in the index. */
+	/**
+	 * Create a new {@code BitmapBuilder} based on the values in the index.
+	 *
+	 * @return a new {@code BitmapBuilder} based on the values in the index.
+	 */
 	BitmapBuilder newBitmapBuilder();
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapObject.java

@@ -50,7 +50,7 @@ package org.eclipse.jgit.lib;
  */
 public abstract class BitmapObject {
 	/**
-	 * Get Git object type. See {@link Constants}.
+	 * Get Git object type. See {@link org.eclipse.jgit.lib.Constants}.
 	 *
 	 * @return object type
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java

@@ -73,7 +73,7 @@ public class BlobBasedConfig extends Config {
 	 *            the base configuration file
 	 * @param blob
 	 *            the byte array, should be UTF-8 encoded text.
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             the byte array is not a valid configuration format.
 	 */
 	public BlobBasedConfig(Config base, final byte[] blob)
@@ -98,9 +98,9 @@ public class BlobBasedConfig extends Config {
 	 *            the repository
 	 * @param objectId
 	 *            the object identifier
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the blob cannot be read from the repository.
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             the blob is not a valid configuration format.
 	 */
 	public BlobBasedConfig(Config base, Repository db, AnyObjectId objectId)
@@ -134,11 +134,11 @@ public class BlobBasedConfig extends Config {
 	 *            the tree (or commit) that contains the object
 	 * @param path
 	 *            the path within the tree
-	 * @throws FileNotFoundException
+	 * @throws java.io.FileNotFoundException
 	 *             the path does not exist in the commit's tree.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the tree and/or blob cannot be accessed.
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             the blob is not a valid configuration format.
 	 */
 	public BlobBasedConfig(Config base, Repository db, AnyObjectId treeish,

org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobObjectChecker.java

@@ -85,7 +85,7 @@ public interface BlobObjectChecker {
 	 *
 	 * @param id
 	 *            identity of the object being checked.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 */
 	void endBlob(AnyObjectId id) throws CorruptObjectException;

org.eclipse.jgit/src/org/eclipse/jgit/lib/BranchConfig.java

@@ -113,6 +113,8 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Get the full tracking branch name
+	 *
 	 * @return the full tracking branch name or <code>null</code> if it could
 	 *         not be determined
 	 */
@@ -129,6 +131,8 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Get the full remote-tracking branch name
+	 *
 	 * @return the full remote-tracking branch name or {@code null} if it could
 	 *         not be determined. If you also want local tracked branches use
 	 *         {@link #getTrackingBranch()} instead.
@@ -143,6 +147,9 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Whether the "remote" setting points to the local repository (with
+	 * {@value #LOCAL_REPOSITORY})
+	 *
 	 * @return {@code true} if the "remote" setting points to the local
 	 *         repository (with {@value #LOCAL_REPOSITORY}), false otherwise
 	 * @since 3.5
@@ -152,6 +159,8 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Get the remote this branch is configured to fetch from/push to>
+	 *
 	 * @return the remote this branch is configured to fetch from/push to, or
 	 *         {@code null} if not defined
 	 * @since 3.5
@@ -162,6 +171,8 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Get the name of the upstream branch as it is called on the remote
+	 *
 	 * @return the name of the upstream branch as it is called on the remote, or
 	 *         {@code null} if not defined
 	 * @since 3.5
@@ -172,6 +183,8 @@ public class BranchConfig {
 	}
 
 	/**
+	 * Whether the branch is configured to be rebased
+	 *
 	 * @return {@code true} if the branch is configured to be rebased
 	 * @since 3.5
 	 */
@@ -182,7 +195,7 @@ public class BranchConfig {
 	/**
 	 * Retrieves the config value of branch.[name].rebase.
 	 *
-	 * @return the {@link BranchRebaseMode}
+	 * @return the {@link org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode}
 	 * @since 4.5
 	 */
 	public BranchRebaseMode getRebaseMode() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/BranchTrackingStatus.java

@@ -65,7 +65,7 @@ public class BranchTrackingStatus {
 	 * @param branchName
 	 *            the local branch
 	 * @return the tracking status, or null if it is not known
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public static BranchTrackingStatus of(Repository repository, String branchName)
 			throws IOException {
@@ -119,6 +119,8 @@ public class BranchTrackingStatus {
 	}
 
 	/**
+	 * Get full remote-tracking branch name
+	 *
 	 * @return full remote-tracking branch name
 	 */
 	public String getRemoteTrackingBranch() {
@@ -126,6 +128,9 @@ public class BranchTrackingStatus {
 	}
 
 	/**
+	 * Get number of commits that the local branch is ahead of the
+	 * remote-tracking branch
+	 *
 	 * @return number of commits that the local branch is ahead of the
 	 *         remote-tracking branch
 	 */
@@ -134,6 +139,9 @@ public class BranchTrackingStatus {
 	}
 
 	/**
+	 * Get number of commits that the local branch is behind of the
+	 * remote-tracking branch
+	 *
 	 * @return number of commits that the local branch is behind of the
 	 *         remote-tracking branch
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/CheckoutEntry.java

@@ -8,11 +8,15 @@ package org.eclipse.jgit.lib;
 public interface CheckoutEntry {
 
 	/**
+	 * Get the name of the branch before checkout
+	 *
 	 * @return the name of the branch before checkout
 	 */
 	public abstract String getFromBranch();
 
 	/**
+	 * Get the name of the branch after checkout
+	 *
 	 * @return the name of the branch after checkout
 	 */
 	public abstract String getToBranch();

org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java

@@ -88,13 +88,19 @@ public class CommitBuilder {
 
 	private Charset encoding;
 
-	/** Initialize an empty commit. */
+	/**
+	 * Initialize an empty commit.
+	 */
 	public CommitBuilder() {
 		parentIds = EMPTY_OBJECTID_LIST;
 		encoding = Constants.CHARSET;
 	}
 
-	/** @return id of the root tree listing this commit's snapshot. */
+	/**
+	 * Get id of the root tree listing this commit's snapshot.
+	 *
+	 * @return id of the root tree listing this commit's snapshot.
+	 */
 	public ObjectId getTreeId() {
 		return treeId;
 	}
@@ -109,7 +115,11 @@ public class CommitBuilder {
 		treeId = id.copy();
 	}
 
-	/** @return the author of this commit (who wrote it). */
+	/**
+	 * Get the author of this commit (who wrote it).
+	 *
+	 * @return the author of this commit (who wrote it).
+	 */
 	public PersonIdent getAuthor() {
 		return author;
 	}
@@ -124,7 +134,11 @@ public class CommitBuilder {
 		author = newAuthor;
 	}
 
-	/** @return the committer and commit time for this object. */
+	/**
+	 * Get the committer and commit time for this object.
+	 *
+	 * @return the committer and commit time for this object.
+	 */
 	public PersonIdent getCommitter() {
 		return committer;
 	}
@@ -139,7 +153,11 @@ public class CommitBuilder {
 		committer = newCommitter;
 	}
 
-	/** @return the ancestors of this commit. Never null. */
+	/**
+	 * Get the ancestors of this commit.
+	 *
+	 * @return the ancestors of this commit. Never null.
+	 */
 	public ObjectId[] getParentIds() {
 		return parentIds;
 	}
@@ -210,7 +228,11 @@ public class CommitBuilder {
 		}
 	}
 
-	/** @return the complete commit message. */
+	/**
+	 * Get the complete commit message.
+	 *
+	 * @return the complete commit message.
+	 */
 	public String getMessage() {
 		return message;
 	}
@@ -229,7 +251,8 @@ public class CommitBuilder {
 	 * Set the encoding for the commit information
 	 *
 	 * @param encodingName
-	 *            the encoding name. See {@link Charset#forName(String)}.
+	 *            the encoding name. See
+	 *            {@link java.nio.charset.Charset#forName(String)}.
 	 */
 	public void setEncoding(String encodingName) {
 		encoding = Charset.forName(encodingName);
@@ -245,7 +268,11 @@ public class CommitBuilder {
 		encoding = enc;
 	}
 
-	/** @return the encoding that should be used for the commit message text. */
+	/**
+	 * Get the encoding that should be used for the commit message text.
+	 *
+	 * @return the encoding that should be used for the commit message text.
+	 */
 	public Charset getEncoding() {
 		return encoding;
 	}
@@ -255,7 +282,7 @@ public class CommitBuilder {
 	 *
 	 * @return this object in the canonical commit format, suitable for storage
 	 *         in a repository.
-	 * @throws UnsupportedEncodingException
+	 * @throws java.io.UnsupportedEncodingException
 	 *             the encoding specified by {@link #getEncoding()} is not
 	 *             supported by this Java runtime.
 	 */
@@ -314,7 +341,7 @@ public class CommitBuilder {
 	 *
 	 * @return this object in the canonical commit format, suitable for storage
 	 *         in a repository.
-	 * @throws UnsupportedEncodingException
+	 * @throws java.io.UnsupportedEncodingException
 	 *             the encoding specified by {@link #getEncoding()} is not
 	 *             supported by this Java runtime.
 	 */
@@ -322,6 +349,7 @@ public class CommitBuilder {
 		return build();
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java

@@ -108,7 +108,9 @@ public class Config {
 	 */
 	static final String MAGIC_EMPTY_VALUE = new String();
 
-	/** Create a configuration with no default fallback. */
+	/**
+	 * Create a configuration with no default fallback.
+	 */
 	public Config() {
 		this(null);
 	}
@@ -126,8 +128,8 @@ public class Config {
 	}
 
 	/**
-	 * Globally sets a {@link TypedConfigGetter} that is subsequently used to
-	 * read typed values from all git configs.
+	 * Globally sets a {@link org.eclipse.jgit.lib.TypedConfigGetter} that is
+	 * subsequently used to read typed values from all git configs.
 	 *
 	 * @param getter
 	 *            to use; if {@code null} use the default getter.
@@ -340,8 +342,6 @@ public class Config {
 	/**
 	 * Parse an enumeration from the configuration.
 	 *
-	 * @param <T>
-	 *            type of the enumeration object.
 	 * @param section
 	 *            section the key is grouped within.
 	 * @param subsection
@@ -374,8 +374,6 @@ public class Config {
 	/**
 	 * Parse an enumeration from the configuration.
 	 *
-	 * @param <T>
-	 *            type of the enumeration object.
 	 * @param all
 	 *            all possible values in the enumeration which should be
 	 *            recognized. Typically {@code EnumType.values()}.
@@ -471,7 +469,8 @@ public class Config {
 	}
 
 	/**
-	 * Parse a list of {@link RefSpec}s from the configuration.
+	 * Parse a list of {@link org.eclipse.jgit.transport.RefSpec}s from the
+	 * configuration.
 	 *
 	 * @param section
 	 *            section the key is in.
@@ -479,7 +478,8 @@ public class Config {
 	 *            subsection the key is in, or null if not in a subsection.
 	 * @param name
 	 *            the key name.
-	 * @return a possibly empty list of {@link RefSpec}s
+	 * @return a possibly empty list of
+	 *         {@link org.eclipse.jgit.transport.RefSpec}s
 	 * @since 4.9
 	 */
 	public List<RefSpec> getRefSpecs(String section, String subsection,
@@ -488,6 +488,9 @@ public class Config {
 	}
 
 	/**
+	 * Get set of all subsections of specified section within this configuration
+	 * and its base configuration
+	 *
 	 * @param section
 	 *            section to search for.
 	 * @return set of all subsections of specified section within this
@@ -501,16 +504,20 @@ public class Config {
 	}
 
 	/**
-	 * @return the sections defined in this {@link Config}. The set's iterator
-	 *         returns sections in the order they are declared by the
-	 *         configuration starting from this instance and progressing through
-	 *         the base.
+	 * Get the sections defined in this {@link org.eclipse.jgit.lib.Config}.
+	 *
+	 * @return the sections defined in this {@link org.eclipse.jgit.lib.Config}.
+	 *         The set's iterator returns sections in the order they are
+	 *         declared by the configuration starting from this instance and
+	 *         progressing through the base.
 	 */
 	public Set<String> getSections() {
 		return getState().getSections();
 	}
 
 	/**
+	 * Get the list of names defined for this section
+	 *
 	 * @param section
 	 *            the section
 	 * @return the list of names defined for this section
@@ -520,6 +527,8 @@ public class Config {
 	}
 
 	/**
+	 * Get the list of names defined for this subsection
+	 *
 	 * @param section
 	 *            the section
 	 * @param subsection
@@ -531,6 +540,8 @@ public class Config {
 	}
 
 	/**
+	 * Get the list of names defined for this section
+	 *
 	 * @param section
 	 *            the section
 	 * @param recursive
@@ -544,6 +555,8 @@ public class Config {
 	}
 
 	/**
+	 * Get the list of names defined for this section
+	 *
 	 * @param section
 	 *            the section
 	 * @param subsection
@@ -600,7 +613,8 @@ public class Config {
 	 * Adds a listener to be notified about changes.
 	 * <p>
 	 * Clients are supposed to remove the listeners after they are done with
-	 * them using the {@link ListenerHandle#remove()} method
+	 * them using the {@link org.eclipse.jgit.events.ListenerHandle#remove()}
+	 * method
 	 *
 	 * @param listener
 	 *            the listener
@@ -755,8 +769,6 @@ public class Config {
 	 *         name = value
 	 * </pre>
 	 *
-	 * @param <T>
-	 *            type of the enumeration object.
 	 * @param section
 	 *            section name, e.g "branch"
 	 * @param subsection
@@ -976,6 +988,8 @@ public class Config {
 	}
 
 	/**
+	 * Get this configuration, formatted as a Git style text file.
+	 *
 	 * @return this configuration, formatted as a Git style text file.
 	 */
 	public String toText() {
@@ -1025,7 +1039,7 @@ public class Config {
 	 *
 	 * @param text
 	 *            Git style text file listing configuration properties.
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             the text supplied is not formatted correctly. No changes were
 	 *             made to {@code this}.
 	 */
@@ -1114,7 +1128,7 @@ public class Config {
 	 *            possibly relative path to the included config, as specified in
 	 *            this config
 	 * @return the read bytes, or null if the included config should be ignored
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             if something went wrong while reading the config
 	 * @since 4.10
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigLine.java

@@ -112,6 +112,7 @@ class ConfigLine {
 		return a.equals(b);
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java

@@ -55,7 +55,9 @@ import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.util.MutableInteger;
 
-/** Misc. constants used throughout JGit. */
+/**
+ * Misc. constants used throughout JGit.
+ */
 @SuppressWarnings("nls")
 public final class Constants {
 	/** Hash function used natively by Git for all objects. */
@@ -446,7 +448,7 @@ public final class Constants {
 	 * Create a new digest function for objects.
 	 *
 	 * @return a new digest object.
-	 * @throws RuntimeException
+	 * @throws java.lang.RuntimeException
 	 *             this Java virtual machine does not support the required hash
 	 *             function. Very unlikely given that JGit uses a hash function
 	 *             that is in the Java reference specification.
@@ -524,7 +526,7 @@ public final class Constants {
 	 *            <code>endMark</code> when the parse is successful.
 	 * @return a type code constant (one of {@link #OBJ_BLOB},
 	 *         {@link #OBJ_COMMIT}, {@link #OBJ_TAG}, {@link #OBJ_TREE}.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             there is no valid type identified by <code>typeString</code>.
 	 */
 	public static int decodeTypeString(final AnyObjectId id,
@@ -602,7 +604,7 @@ public final class Constants {
 	 *            127 (outside of 7-bit ASCII).
 	 * @return a byte array of the same length as the input string, holding the
 	 *         same characters, in the same order.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the input string contains one or more characters outside of
 	 *             the 7-bit ASCII character space.
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/CoreConfig.java

@@ -180,6 +180,8 @@ public class CoreConfig {
 	}
 
 	/**
+	 * Get the compression level to use when storing loose objects
+	 *
 	 * @return The compression level to use when storing loose objects
 	 */
 	public int getCompression() {
@@ -187,6 +189,8 @@ public class CoreConfig {
 	}
 
 	/**
+	 * Get the preferred pack index file format; 0 for oldest possible.
+	 *
 	 * @return the preferred pack index file format; 0 for oldest possible.
 	 */
 	public int getPackIndexVersion() {
@@ -194,6 +198,8 @@ public class CoreConfig {
 	}
 
 	/**
+	 * Whether to log all refUpdates
+	 *
 	 * @return whether to log all refUpdates
 	 */
 	public boolean isLogAllRefUpdates() {
@@ -201,6 +207,8 @@ public class CoreConfig {
 	}
 
 	/**
+	 * Get path of excludesfile
+	 *
 	 * @return path of excludesfile
 	 */
 	public String getExcludesFile() {
@@ -208,6 +216,8 @@ public class CoreConfig {
 	}
 
 	/**
+	 * Get path of attributesfile
+	 *
 	 * @return path of attributesfile
 	 * @since 3.7
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java

@@ -57,13 +57,14 @@ import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.util.StringUtils;
 
 /**
- * An {@link TypedConfigGetter} that throws {@link IllegalArgumentException} on
- * invalid values.
+ * An {@link org.eclipse.jgit.lib.TypedConfigGetter} that throws
+ * {@link java.lang.IllegalArgumentException} on invalid values.
  *
  * @since 4.9
  */
 public class DefaultTypedConfigGetter implements TypedConfigGetter {
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean getBoolean(Config config, String section, String subsection,
 			String name, boolean defaultValue) {
@@ -82,6 +83,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public <T extends Enum<?>> T getEnum(Config config, T[] all, String section,
 			String subsection, String name, T defaultValue) {
@@ -139,6 +141,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getInt(Config config, String section, String subsection,
 			String name, int defaultValue) {
@@ -150,6 +153,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 				.format(JGitText.get().integerValueOutOfRange, section, name));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getLong(Config config, String section, String subsection,
 			String name, long defaultValue) {
@@ -187,6 +191,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public long getTimeUnit(Config config, String section, String subsection,
 			String name, long defaultValue, TimeUnit wantUnit) {
@@ -286,6 +291,7 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 						section, name, valueString));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public @NonNull List<RefSpec> getRefSpecs(Config config, String section,
 			String subsection, String name) {

org.eclipse.jgit/src/org/eclipse/jgit/lib/EmptyProgressMonitor.java

@@ -51,26 +51,31 @@ package org.eclipse.jgit.lib;
  */
 public abstract class EmptyProgressMonitor implements ProgressMonitor {
 
+	/** {@inheritDoc} */
 	@Override
 	public void start(int totalTasks) {
 		// empty
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void beginTask(String title, int totalWork) {
 		// empty
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void update(int completed) {
 		// empty
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void endTask() {
 		// empty
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCancelled() {
 		return false;

org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java

@@ -82,7 +82,9 @@ public abstract class FileMode {
 	/** Bit pattern for {@link #TYPE_MASK} matching {@link #MISSING}. */
 	public static final int TYPE_MISSING = 0000000;
 
-	/** Mode indicating an entry is a tree (aka directory). */
+	/**
+	 * Mode indicating an entry is a tree (aka directory).
+	 */
 	public static final FileMode TREE = new FileMode(TYPE_TREE,
 			Constants.OBJ_TREE) {
 		@Override
@@ -197,9 +199,11 @@ public abstract class FileMode {
 	}
 
 	/**
-	 * Test a file mode for equality with this {@link FileMode} object.
+	 * Test a file mode for equality with this
+	 * {@link org.eclipse.jgit.lib.FileMode} object.
 	 *
 	 * @param modebits
+	 *            a int.
 	 * @return true if the mode bits represent the same mode as this object
 	 */
 	public abstract boolean equals(final int modebits);
@@ -215,7 +219,7 @@ public abstract class FileMode {
 	 *
 	 * @param os
 	 *            stream to copy the mode to.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream encountered an error during the copy.
 	 */
 	public void copyTo(final OutputStream os) throws IOException {
@@ -240,6 +244,8 @@ public abstract class FileMode {
 	}
 
 	/**
+	 * Copy the number of bytes written by {@link #copyTo(OutputStream)}.
+	 *
 	 * @return the number of bytes written by {@link #copyTo(OutputStream)}.
 	 */
 	public int copyToLength() {
@@ -249,7 +255,7 @@ public abstract class FileMode {
 	/**
 	 * Get the object type that should appear for this type of mode.
 	 * <p>
-	 * See the object type constants in {@link Constants}.
+	 * See the object type constants in {@link org.eclipse.jgit.lib.Constants}.
 	 *
 	 * @return one of the well known object type constants.
 	 */
@@ -257,13 +263,19 @@ public abstract class FileMode {
 		return objectType;
 	}
 
-	/** Format this mode as an octal string (for debugging only). */
+	/**
+	 * {@inheritDoc}
+	 * <p>
+	 * Format this mode as an octal string (for debugging only).
+	 */
 	@Override
 	public String toString() {
 		return Integer.toOctalString(modeBits);
 	}
 
 	/**
+	 * Get the mode bits as an integer.
+	 *
 	 * @return The mode bits as an integer.
 	 */
 	public int getBits() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java

@@ -285,12 +285,13 @@ public class IndexDiff {
 	 * Construct an IndexDiff
 	 *
 	 * @param repository
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 * @param revstr
-	 *            symbolic name e.g. HEAD
-	 *            An EmptyTreeIterator is used if <code>revstr</code> cannot be resolved.
+	 *            symbolic name e.g. HEAD An EmptyTreeIterator is used if
+	 *            <code>revstr</code> cannot be resolved.
 	 * @param workingTreeIterator
 	 *            iterator for working directory
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public IndexDiff(Repository repository, String revstr,
 			WorkingTreeIterator workingTreeIterator) throws IOException {
@@ -301,11 +302,12 @@ public class IndexDiff {
 	 * Construct an Indexdiff
 	 *
 	 * @param repository
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 * @param objectId
 	 *            tree id. If null, an EmptyTreeIterator is used.
 	 * @param workingTreeIterator
 	 *            iterator for working directory
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public IndexDiff(Repository repository, ObjectId objectId,
 			WorkingTreeIterator workingTreeIterator) throws IOException {
@@ -321,6 +323,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Defines how modifications in submodules are treated
+	 *
 	 * @param mode
 	 *            defines how modifications in submodules are treated
 	 * @since 3.6
@@ -336,7 +340,8 @@ public class IndexDiff {
 	public interface WorkingTreeIteratorFactory {
 		/**
 		 * @param repo
-		 * @return a WorkingTreeIterator for repo
+		 *            the repository
+		 * @return working tree iterator
 		 */
 		public WorkingTreeIterator getWorkingTreeIterator(Repository repo);
 	}
@@ -363,6 +368,7 @@ public class IndexDiff {
 	 * files.
 	 *
 	 * @param filter
+	 *            a {@link org.eclipse.jgit.treewalk.filter.TreeFilter} object.
 	 */
 	public void setFilter(TreeFilter filter) {
 		this.filter = filter;
@@ -374,7 +380,7 @@ public class IndexDiff {
 	 * monitor is required.
 	 *
 	 * @return if anything is different between index, tree, and workdir
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public boolean diff() throws IOException {
 		return diff(null, 0, 0, ""); //$NON-NLS-1$
@@ -396,10 +402,9 @@ public class IndexDiff {
 	 *            number or estimated files in the working tree
 	 * @param estIndexSize
 	 *            number of estimated entries in the cache
-	 * @param title
-	 *
+	 * @param title a {@link java.lang.String} object.
 	 * @return if anything is different between index, tree, and workdir
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public boolean diff(final ProgressMonitor monitor, int estWorkTreeSize,
 			int estIndexSize, final String title)
@@ -621,6 +626,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files added to the index, not in the tree
+	 *
 	 * @return list of files added to the index, not in the tree
 	 */
 	public Set<String> getAdded() {
@@ -628,6 +635,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files changed from tree to index
+	 *
 	 * @return list of files changed from tree to index
 	 */
 	public Set<String> getChanged() {
@@ -635,6 +644,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files removed from index, but in tree
+	 *
 	 * @return list of files removed from index, but in tree
 	 */
 	public Set<String> getRemoved() {
@@ -642,6 +653,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files in index, but not filesystem
+	 *
 	 * @return list of files in index, but not filesystem
 	 */
 	public Set<String> getMissing() {
@@ -649,6 +662,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files modified on disk relative to the index
+	 *
 	 * @return list of files modified on disk relative to the index
 	 */
 	public Set<String> getModified() {
@@ -656,6 +671,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files that are not ignored, and not in the index.
+	 *
 	 * @return list of files that are not ignored, and not in the index.
 	 */
 	public Set<String> getUntracked() {
@@ -663,6 +680,9 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files that are in conflict, corresponds to the keys of
+	 * {@link #getConflictingStageStates()}
+	 *
 	 * @return list of files that are in conflict, corresponds to the keys of
 	 *         {@link #getConflictingStageStates()}
 	 */
@@ -671,8 +691,11 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get the map from each path of {@link #getConflicting()} to its
+	 * corresponding {@link org.eclipse.jgit.lib.IndexDiff.StageState}
+	 *
 	 * @return the map from each path of {@link #getConflicting()} to its
-	 *         corresponding {@link StageState}
+	 *         corresponding {@link org.eclipse.jgit.lib.IndexDiff.StageState}
 	 * @since 3.0
 	 */
 	public Map<String, StageState> getConflictingStageStates() {
@@ -693,6 +716,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of files with the flag assume-unchanged
+	 *
 	 * @return list of files with the flag assume-unchanged
 	 */
 	public Set<String> getAssumeUnchanged() {
@@ -707,6 +732,8 @@ public class IndexDiff {
 	}
 
 	/**
+	 * Get list of folders containing only untracked files/folders
+	 *
 	 * @return list of folders containing only untracked files/folders
 	 */
 	public Set<String> getUntrackedFolders() {
@@ -717,7 +744,7 @@ public class IndexDiff {
 	/**
 	 * Get the file mode of the given path in the index
 	 *
-	 * @param path
+	 * @param path a {@link java.lang.String} object.
 	 * @return file mode
 	 */
 	public FileMode getIndexMode(final String path) {
@@ -729,7 +756,7 @@ public class IndexDiff {
 	 * Get the list of paths that IndexDiff has detected to differ and have the
 	 * given file mode
 	 *
-	 * @param mode
+	 * @param mode a {@link org.eclipse.jgit.lib.FileMode} object.
 	 * @return the list of paths that IndexDiff has detected to differ and have
 	 *         the given file mode
 	 * @since 3.6

org.eclipse.jgit/src/org/eclipse/jgit/lib/InflaterCache.java

@@ -46,7 +46,9 @@ package org.eclipse.jgit.lib;
 
 import java.util.zip.Inflater;
 
-/** Creates zlib based inflaters as necessary for object decompression. */
+/**
+ * Creates zlib based inflaters as necessary for object decompression.
+ */
 public class InflaterCache {
 	private static final int SZ = 4;
 

org.eclipse.jgit/src/org/eclipse/jgit/lib/MutableObjectId.java

@@ -79,15 +79,17 @@ public class MutableObjectId extends AnyObjectId {
 	 *
 	 * @param index
 	 *            index of the byte to set in the raw form of the ObjectId. Must
-	 *            be in range [0, {@link Constants#OBJECT_ID_LENGTH}).
+	 *            be in range [0,
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}).
 	 * @param value
 	 *            the value of the specified byte at {@code index}. Values are
 	 *            unsigned and thus are in the range [0,255] rather than the
 	 *            signed byte range of [-128, 127].
-	 * @throws ArrayIndexOutOfBoundsException
+	 * @throws java.lang.ArrayIndexOutOfBoundsException
 	 *             {@code index} is less than 0, equal to
-	 *             {@link Constants#OBJECT_ID_LENGTH}, or greater than
-	 *             {@link Constants#OBJECT_ID_LENGTH}.
+	 *             {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}, or
+	 *             greater than
+	 *             {@link org.eclipse.jgit.lib.Constants#OBJECT_ID_LENGTH}.
 	 */
 	public void setByte(int index, int value) {
 		switch (index >> 2) {
@@ -128,7 +130,9 @@ public class MutableObjectId extends AnyObjectId {
 		}
 	}
 
-	/** Make this id match {@link ObjectId#zeroId()}. */
+	/**
+	 * Make this id match {@link org.eclipse.jgit.lib.ObjectId#zeroId()}.
+	 */
 	public void clear() {
 		w1 = 0;
 		w2 = 0;
@@ -198,7 +202,6 @@ public class MutableObjectId extends AnyObjectId {
 	 *            must be available within this integers array.
 	 * @param p
 	 *            position to read the first integer of data from.
-	 *
 	 */
 	public void fromRaw(final int[] ints, final int p) {
 		w1 = ints[p];
@@ -212,10 +215,15 @@ public class MutableObjectId extends AnyObjectId {
 	 * Convert an ObjectId from binary representation expressed in integers.
 	 *
 	 * @param a
+	 *            an int.
 	 * @param b
+	 *            an int.
 	 * @param c
+	 *            an int.
 	 * @param d
+	 *            an int.
 	 * @param e
+	 *            an int.
 	 * @since 4.7
 	 */
 	public void set(int a, int b, int c, int d, int e) {
@@ -265,6 +273,7 @@ public class MutableObjectId extends AnyObjectId {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId toObjectId() {
 		return new ObjectId(this);

org.eclipse.jgit/src/org/eclipse/jgit/lib/NullProgressMonitor.java

@@ -56,26 +56,31 @@ public class NullProgressMonitor implements ProgressMonitor {
 		// Do not let others instantiate
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void start(int totalTasks) {
 		// Do not report.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void beginTask(String title, int totalWork) {
 		// Do not report.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void update(int completed) {
 		// Do not report.
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCancelled() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void endTask() {
 		// Do not report.

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java

@@ -317,12 +317,12 @@ public class ObjectChecker {
 	 *
 	 * @param objType
 	 *            type of the object. Must be a valid object type code in
-	 *            {@link Constants}.
+	 *            {@link org.eclipse.jgit.lib.Constants}.
 	 * @param raw
 	 *            the raw data which comprises the object. This should be in the
 	 *            canonical format (that is the format used to generate the
 	 *            ObjectId of the object). The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if an error is identified.
 	 */
 	public void check(int objType, byte[] raw)
@@ -337,12 +337,12 @@ public class ObjectChecker {
 	 *            identify of the object being checked.
 	 * @param objType
 	 *            type of the object. Must be a valid object type code in
-	 *            {@link Constants}.
+	 *            {@link org.eclipse.jgit.lib.Constants}.
 	 * @param raw
 	 *            the raw data which comprises the object. This should be in the
 	 *            canonical format (that is the format used to generate the
 	 *            ObjectId of the object). The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if an error is identified.
 	 * @since 4.2
 	 */
@@ -449,7 +449,7 @@ public class ObjectChecker {
 	 *
 	 * @param raw
 	 *            the commit data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 */
 	public void checkCommit(byte[] raw) throws CorruptObjectException {
@@ -463,7 +463,7 @@ public class ObjectChecker {
 	 *            identity of the object being checked.
 	 * @param raw
 	 *            the commit data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 * @since 4.2
 	 */
@@ -503,7 +503,7 @@ public class ObjectChecker {
 	 *
 	 * @param raw
 	 *            the tag data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 */
 	public void checkTag(byte[] raw) throws CorruptObjectException {
@@ -517,7 +517,7 @@ public class ObjectChecker {
 	 *            identity of the object being checked.
 	 * @param raw
 	 *            the tag data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 * @since 4.2
 	 */
@@ -593,7 +593,7 @@ public class ObjectChecker {
 	 *
 	 * @param raw
 	 *            the raw tree data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 */
 	public void checkTree(byte[] raw) throws CorruptObjectException {
@@ -607,7 +607,7 @@ public class ObjectChecker {
 	 *            identity of the object being checked.
 	 * @param raw
 	 *            the raw tree data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 * @since 4.2
 	 */
@@ -739,11 +739,13 @@ public class ObjectChecker {
 	/**
 	 * Check tree path entry for validity.
 	 * <p>
-	 * Unlike {@link #checkPathSegment(byte[], int, int)}, this version
-	 * scans a multi-directory path string such as {@code "src/main.c"}.
+	 * Unlike {@link #checkPathSegment(byte[], int, int)}, this version scans a
+	 * multi-directory path string such as {@code "src/main.c"}.
 	 *
-	 * @param path path string to scan.
-	 * @throws CorruptObjectException path is invalid.
+	 * @param path
+	 *            path string to scan.
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
+	 *             path is invalid.
 	 * @since 3.6
 	 */
 	public void checkPath(String path) throws CorruptObjectException {
@@ -754,13 +756,17 @@ public class ObjectChecker {
 	/**
 	 * Check tree path entry for validity.
 	 * <p>
-	 * Unlike {@link #checkPathSegment(byte[], int, int)}, this version
-	 * scans a multi-directory path string such as {@code "src/main.c"}.
+	 * Unlike {@link #checkPathSegment(byte[], int, int)}, this version scans a
+	 * multi-directory path string such as {@code "src/main.c"}.
 	 *
-	 * @param raw buffer to scan.
-	 * @param ptr offset to first byte of the name.
-	 * @param end offset to one past last byte of name.
-	 * @throws CorruptObjectException path is invalid.
+	 * @param raw
+	 *            buffer to scan.
+	 * @param ptr
+	 *            offset to first byte of the name.
+	 * @param end
+	 *            offset to one past last byte of name.
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
+	 *             path is invalid.
 	 * @since 3.6
 	 */
 	public void checkPath(byte[] raw, int ptr, int end)
@@ -778,10 +784,14 @@ public class ObjectChecker {
 	/**
 	 * Check tree path entry for validity.
 	 *
-	 * @param raw buffer to scan.
-	 * @param ptr offset to first byte of the name.
-	 * @param end offset to one past last byte of name.
-	 * @throws CorruptObjectException name is invalid.
+	 * @param raw
+	 *            buffer to scan.
+	 * @param ptr
+	 *            offset to first byte of the name.
+	 * @param end
+	 *            offset to one past last byte of name.
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
+	 *             name is invalid.
 	 * @since 3.4
 	 */
 	public void checkPathSegment(byte[] raw, int ptr, int end)
@@ -1073,7 +1083,7 @@ public class ObjectChecker {
 	}
 
 	/**
-	 * Create a new {@link BlobObjectChecker}.
+	 * Create a new {@link org.eclipse.jgit.lib.BlobObjectChecker}.
 	 *
 	 * @return new BlobObjectChecker or null if it's not provided.
 	 * @since 4.9
@@ -1086,12 +1096,13 @@ public class ObjectChecker {
 	/**
 	 * Check a blob for errors.
 	 *
-	 * <p>This may not be called from PackParser in some cases. Use {@link
-	 * #newBlobObjectChecker} instead.
+	 * <p>
+	 * This may not be called from PackParser in some cases. Use
+	 * {@link #newBlobObjectChecker} instead.
 	 *
 	 * @param raw
 	 *            the blob data. The array is never modified.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             if any error was detected.
 	 */
 	public void checkBlob(final byte[] raw) throws CorruptObjectException {

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectDatabase.java

@@ -52,10 +52,12 @@ import org.eclipse.jgit.errors.MissingObjectException;
  * Abstraction of arbitrary object storage.
  * <p>
  * An object database stores one or more Git objects, indexed by their unique
- * {@link ObjectId}.
+ * {@link org.eclipse.jgit.lib.ObjectId}.
  */
 public abstract class ObjectDatabase {
-	/** Initialize a new database instance for access. */
+	/**
+	 * Initialize a new database instance for access.
+	 */
 	protected ObjectDatabase() {
 		// Protected to force extension.
 	}
@@ -73,7 +75,7 @@ public abstract class ObjectDatabase {
 	/**
 	 * Initialize a new object database at this location.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database could not be created.
 	 */
 	public void create() throws IOException {
@@ -116,7 +118,7 @@ public abstract class ObjectDatabase {
 	 * @param objectId
 	 *            identity of the object to test for existence of.
 	 * @return true if the specified object is stored in this database.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public boolean has(final AnyObjectId objectId) throws IOException {
@@ -133,10 +135,10 @@ public abstract class ObjectDatabase {
 	 *
 	 * @param objectId
 	 *            identity of the object to open.
-	 * @return a {@link ObjectLoader} for accessing the object.
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the object.
 	 * @throws MissingObjectException
 	 *             the object does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open(final AnyObjectId objectId)
@@ -154,16 +156,17 @@ public abstract class ObjectDatabase {
 	 *            identity of the object to open.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
-	 *            {@link Constants#OBJ_BLOB}; {@link ObjectReader#OBJ_ANY} if
-	 *            the object type is not known, or does not matter to the
-	 *            caller.
-	 * @return a {@link ObjectLoader} for accessing the object.
-	 * @throws MissingObjectException
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB};
+	 *            {@link org.eclipse.jgit.lib.ObjectReader#OBJ_ANY} if the
+	 *            object type is not known, or does not matter to the caller.
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the
+	 *         object.
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open(AnyObjectId objectId, int typeHint)

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java

@@ -252,10 +252,15 @@ public class ObjectId extends AnyObjectId implements Serializable {
 	 * Construct an ObjectId from 160 bits provided in 5 words.
 	 *
 	 * @param new_1
+	 *            an int
 	 * @param new_2
+	 *            an int
 	 * @param new_3
+	 *            an int
 	 * @param new_4
+	 *            an int
 	 * @param new_5
+	 *            an int
 	 * @since 4.7
 	 */
 	public ObjectId(int new_1, int new_2, int new_3, int new_4, int new_5) {
@@ -284,6 +289,7 @@ public class ObjectId extends AnyObjectId implements Serializable {
 		w5 = src.w5;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public ObjectId toObjectId() {
 		return this;

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdOwnerMap.java

@@ -48,10 +48,12 @@ import java.util.Iterator;
 import java.util.NoSuchElementException;
 
 /**
- * Fast, efficient map for {@link ObjectId} subclasses in only one map.
+ * Fast, efficient map for {@link org.eclipse.jgit.lib.ObjectId} subclasses in
+ * only one map.
  * <p>
  * To use this map type, applications must have their entry value type extend
- * from {@link ObjectIdOwnerMap.Entry}, which itself extends from ObjectId.
+ * from {@link org.eclipse.jgit.lib.ObjectIdOwnerMap.Entry}, which itself
+ * extends from ObjectId.
  * <p>
  * Object instances may only be stored in <b>ONE</b> ObjectIdOwnerMap. This
  * restriction exists because the map stores internal map state within each
@@ -59,10 +61,11 @@ import java.util.NoSuchElementException;
  * could corrupt one or both map's internal state.
  * <p>
  * If an object instance must be in more than one map, applications may use
- * ObjectIdOwnerMap for one of the maps, and {@link ObjectIdSubclassMap} for the
- * other map(s). It is encouraged to use ObjectIdOwnerMap for the map that is
- * accessed most often, as this implementation runs faster than the more general
- * ObjectIdSubclassMap implementation.
+ * ObjectIdOwnerMap for one of the maps, and
+ * {@link org.eclipse.jgit.lib.ObjectIdSubclassMap} for the other map(s). It is
+ * encouraged to use ObjectIdOwnerMap for the map that is accessed most often,
+ * as this implementation runs faster than the more general ObjectIdSubclassMap
+ * implementation.
  *
  * @param <V>
  *            type of subclass of ObjectId that will be stored in the map.
@@ -97,7 +100,9 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 	/** Low bit mask to index into {@link #directory}, {@code 2^bits-1}. */
 	private int mask;
 
-	/** Create an empty map. */
+	/**
+	 * Create an empty map.
+	 */
 	@SuppressWarnings("unchecked")
 	public ObjectIdOwnerMap() {
 		bits = 0;
@@ -108,7 +113,9 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 		directory[0] = newSegment();
 	}
 
-	/** Remove all entries from this map. */
+	/**
+	 * Remove all entries from this map.
+	 */
 	public void clear() {
 		size = 0;
 
@@ -137,11 +144,9 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Returns true if this map contains the specified object.
-	 *
-	 * @param toFind
-	 *            object to find.
-	 * @return true if the mapping exists for this object; false otherwise.
 	 */
 	@Override
 	public boolean contains(final AnyObjectId toFind) {
@@ -157,8 +162,6 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 	 *
 	 * @param newValue
 	 *            the object to store.
-	 * @param <Q>
-	 *            type of instance to store.
 	 */
 	public <Q extends V> void add(final Q newValue) {
 		if (++size == grow)
@@ -189,8 +192,6 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 	 * @return {@code newValue} if stored, or the prior value already stored and
 	 *         that would have been returned had the caller used
 	 *         {@code get(newValue)} first.
-	 * @param <Q>
-	 *            type of instance to store.
 	 */
 	@SuppressWarnings("unchecked")
 	public <Q extends V> V addIfAbsent(final Q newValue) {
@@ -210,16 +211,25 @@ public class ObjectIdOwnerMap<V extends ObjectIdOwnerMap.Entry>
 		return newValue;
 	}
 
-	/** @return number of objects in this map. */
+	/**
+	 * Get number of objects in this map.
+	 *
+	 * @return number of objects in this map.
+	 */
 	public int size() {
 		return size;
 	}
 
-	/** @return true if {@link #size()} is 0. */
+	/**
+	 * Whether this map is empty
+	 *
+	 * @return true if {@link #size()} is 0.
+	 */
 	public boolean isEmpty() {
 		return size == 0;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<V> iterator() {
 		return new Iterator<V>() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdRef.java

@@ -47,7 +47,10 @@ package org.eclipse.jgit.lib;
 import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 
-/** A {@link Ref} that points directly at an {@link ObjectId}. */
+/**
+ * A {@link org.eclipse.jgit.lib.Ref} that points directly at an
+ * {@link org.eclipse.jgit.lib.ObjectId}.
+ */
 public abstract class ObjectIdRef implements Ref {
 	/** Any reference whose peeled value is not yet known. */
 	public static class Unpeeled extends ObjectIdRef {
@@ -167,41 +170,48 @@ public abstract class ObjectIdRef implements Ref {
 		this.objectId = id;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public String getName() {
 		return name;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isSymbolic() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Ref getLeaf() {
 		return this;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Ref getTarget() {
 		return this;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@Nullable
 	public ObjectId getObjectId() {
 		return objectId;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Storage getStorage() {
 		return storage;
 	}
 
+	/** {@inheritDoc} */
 	@NonNull
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSet.java

@@ -48,7 +48,8 @@ package org.eclipse.jgit.lib;
  * <p>
  * Usually backed by a read-only data structure such as
  * {@link org.eclipse.jgit.internal.storage.file.PackIndex}. Mutable types like
- * {@link ObjectIdOwnerMap} also implement the interface by checking keys.
+ * {@link org.eclipse.jgit.lib.ObjectIdOwnerMap} also implement the interface by
+ * checking keys.
  *
  * @since 4.2
  */

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java

@@ -49,13 +49,15 @@ import java.util.Iterator;
 import java.util.NoSuchElementException;
 
 /**
- * Fast, efficient map specifically for {@link ObjectId} subclasses.
+ * Fast, efficient map specifically for {@link org.eclipse.jgit.lib.ObjectId}
+ * subclasses.
  * <p>
  * This map provides an efficient translation from any ObjectId instance to a
  * cached subclass of ObjectId that has the same value.
  * <p>
- * If object instances are stored in only one map, {@link ObjectIdOwnerMap} is a
- * more efficient implementation.
+ * If object instances are stored in only one map,
+ * {@link org.eclipse.jgit.lib.ObjectIdOwnerMap} is a more efficient
+ * implementation.
  *
  * @param <V>
  *            type of subclass of ObjectId that will be stored in the map.
@@ -72,12 +74,16 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 
 	V[] table;
 
-	/** Create an empty map. */
+	/**
+	 * Create an empty map.
+	 */
 	public ObjectIdSubclassMap() {
 		initTable(INITIAL_TABLE_SIZE);
 	}
 
-	/** Remove all entries from this map. */
+	/**
+	 * Remove all entries from this map.
+	 */
 	public void clear() {
 		size = 0;
 		initTable(INITIAL_TABLE_SIZE);
@@ -105,11 +111,9 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Returns true if this map contains the specified object.
-	 *
-	 * @param toFind
-	 *            object to find.
-	 * @return true if the mapping exists for this object; false otherwise.
 	 */
 	@Override
 	public boolean contains(final AnyObjectId toFind) {
@@ -126,8 +130,6 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 	 *
 	 * @param newValue
 	 *            the object to store.
-	 * @param <Q>
-	 *            type of instance to store.
 	 */
 	public <Q extends V> void add(final Q newValue) {
 		if (++size == grow)
@@ -152,8 +154,6 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 	 * @return {@code newValue} if stored, or the prior value already stored and
 	 *         that would have been returned had the caller used
 	 *         {@code get(newValue)} first.
-	 * @param <Q>
-	 *            type of instance to store.
 	 */
 	public <Q extends V> V addIfAbsent(final Q newValue) {
 		final int msk = mask;
@@ -177,17 +177,24 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 	}
 
 	/**
+	 * Get number of objects in map
+	 *
 	 * @return number of objects in map
 	 */
 	public int size() {
 		return size;
 	}
 
-	/** @return true if {@link #size()} is 0. */
+	/**
+	 * Whether {@link #size()} is 0.
+	 *
+	 * @return true if {@link #size()} is 0.
+	 */
 	public boolean isEmpty() {
 		return size == 0;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Iterator<V> iterator() {
 		return new Iterator<V>() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectInserter.java

@@ -182,7 +182,9 @@ public abstract class ObjectInserter implements AutoCloseable {
 	/** Temporary working buffer for streaming data through. */
 	private byte[] tempBuffer;
 
-	/** Create a new inserter for a database. */
+	/**
+	 * Create a new inserter for a database.
+	 */
 	protected ObjectInserter() {
 	}
 
@@ -218,6 +220,8 @@ public abstract class ObjectInserter implements AutoCloseable {
 	}
 
 	/**
+	 * Compute digest to help compute an ObjectId
+	 *
 	 * @return digest to help compute an ObjectId
 	 * @since 4.7
 	 */
@@ -272,7 +276,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 *            stream providing the object content. The caller is responsible
 	 *            for closing the stream.
 	 * @return the name of the object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the source stream could not be read.
 	 */
 	public ObjectId idFor(int objectType, long length, InputStream in)
@@ -297,6 +301,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * Compute the ObjectId for the given tree without inserting it.
 	 *
 	 * @param formatter
+	 *            a {@link org.eclipse.jgit.lib.TreeFormatter} object.
 	 * @return the computed ObjectId
 	 */
 	public ObjectId idFor(TreeFormatter formatter) {
@@ -309,7 +314,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * @param formatter
 	 *            the formatter containing the proposed tree's data.
 	 * @return the name of the tree object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored.
 	 */
 	public final ObjectId insert(TreeFormatter formatter) throws IOException {
@@ -325,7 +330,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * @param builder
 	 *            the builder containing the proposed commit's data.
 	 * @return the name of the commit object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored.
 	 */
 	public final ObjectId insert(CommitBuilder builder) throws IOException {
@@ -338,7 +343,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * @param builder
 	 *            the builder containing the proposed tag's data.
 	 * @return the name of the tag object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored.
 	 */
 	public final ObjectId insert(TagBuilder builder) throws IOException {
@@ -353,7 +358,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * @param data
 	 *            complete content of the object.
 	 * @return the name of the object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored.
 	 */
 	public ObjectId insert(final int type, final byte[] data)
@@ -373,7 +378,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * @param len
 	 *            number of bytes to copy from {@code data}.
 	 * @return the name of the object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored.
 	 */
 	public ObjectId insert(int type, byte[] data, int off, int len)
@@ -392,7 +397,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 *            stream providing the object content. The caller is responsible
 	 *            for closing the stream.
 	 * @return the name of the object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object could not be stored, or the source stream could
 	 *             not be read.
 	 */
@@ -406,7 +411,7 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 *            the input stream. The stream is not closed by the parser, and
 	 *            must instead be closed by the caller once parsing is complete.
 	 * @return the pack parser.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the parser instance, which can be configured and then used to
 	 *             parse objects into the ObjectDatabase.
 	 */
@@ -436,13 +441,15 @@ public abstract class ObjectInserter implements AutoCloseable {
 	 * The flush may take some period of time to make the objects available to
 	 * other threads.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the flush could not be completed; objects inserted thus far
 	 *             are in an indeterminate state.
 	 */
 	public abstract void flush() throws IOException;
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Release any resources used by this inserter.
 	 * <p>
 	 * An inserter that has been released can be used again, but may need to be

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectLoader.java

@@ -61,16 +61,23 @@ import org.eclipse.jgit.util.IO;
  */
 public abstract class ObjectLoader {
 	/**
-	 * @return Git in pack object type, see {@link Constants}.
+	 * Get Git in pack object type
+	 *
+	 * @return Git in pack object type, see
+	 *         {@link org.eclipse.jgit.lib.Constants}.
 	 */
 	public abstract int getType();
 
 	/**
+	 * Get size of object in bytes
+	 *
 	 * @return size of object in bytes
 	 */
 	public abstract long getSize();
 
 	/**
+	 * Whether this object is too large to obtain as a byte array.
+	 *
 	 * @return true if this object is too large to obtain as a byte array.
 	 *         Objects over a certain threshold should be accessed only by their
 	 *         {@link #openStream()} to prevent overflowing the JVM heap.
@@ -91,7 +98,7 @@ public abstract class ObjectLoader {
 	 * be modified by the caller.
 	 *
 	 * @return the bytes of this object.
-	 * @throws LargeObjectException
+	 * @throws org.eclipse.jgit.errors.LargeObjectException
 	 *             if the object won't fit into a byte array, because
 	 *             {@link #isLarge()} returns true. Callers should use
 	 *             {@link #openStream()} instead to access the contents.
@@ -113,16 +120,18 @@ public abstract class ObjectLoader {
 	 *
 	 * @param sizeLimit
 	 *            maximum number of bytes to return. If the object is larger
-	 *            than this limit, {@link LargeObjectException} will be thrown.
+	 *            than this limit,
+	 *            {@link org.eclipse.jgit.errors.LargeObjectException} will be
+	 *            thrown.
 	 * @return the bytes of this object.
-	 * @throws LargeObjectException
+	 * @throws org.eclipse.jgit.errors.LargeObjectException
 	 *             if the object is bigger than {@code sizeLimit}, or if
-	 *             {@link OutOfMemoryError} occurs during allocation of the
-	 *             result array. Callers should use {@link #openStream()}
+	 *             {@link java.lang.OutOfMemoryError} occurs during allocation
+	 *             of the result array. Callers should use {@link #openStream()}
 	 *             instead to access the contents.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object is large, and it no longer exists.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public final byte[] getBytes(int sizeLimit) throws LargeObjectException,
@@ -144,7 +153,7 @@ public abstract class ObjectLoader {
 	 * Changes (if made) will affect the cache but not the repository itself.
 	 *
 	 * @return the cached bytes of this object. Do not modify it.
-	 * @throws LargeObjectException
+	 * @throws org.eclipse.jgit.errors.LargeObjectException
 	 *             if the object won't fit into a byte array, because
 	 *             {@link #isLarge()} returns true. Callers should use
 	 *             {@link #openStream()} instead to access the contents.
@@ -167,16 +176,17 @@ public abstract class ObjectLoader {
 	 * @param sizeLimit
 	 *            maximum number of bytes to return. If the object size is
 	 *            larger than this limit and {@link #isLarge()} is true,
-	 *            {@link LargeObjectException} will be thrown.
+	 *            {@link org.eclipse.jgit.errors.LargeObjectException} will be
+	 *            thrown.
 	 * @return the cached bytes of this object. Do not modify it.
-	 * @throws LargeObjectException
+	 * @throws org.eclipse.jgit.errors.LargeObjectException
 	 *             if the object is bigger than {@code sizeLimit}, or if
-	 *             {@link OutOfMemoryError} occurs during allocation of the
-	 *             result array. Callers should use {@link #openStream()}
+	 *             {@link java.lang.OutOfMemoryError} occurs during allocation
+	 *             of the result array. Callers should use {@link #openStream()}
 	 *             instead to access the contents.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object is large, and it no longer exists.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public byte[] getCachedBytes(int sizeLimit) throws LargeObjectException,
@@ -213,9 +223,9 @@ public abstract class ObjectLoader {
 	 * @return a stream of this object's data. Caller must close the stream when
 	 *         through with it. The returned stream is buffered with a
 	 *         reasonable buffer size.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object no longer exists.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public abstract ObjectStream openStream() throws MissingObjectException,
@@ -236,9 +246,9 @@ public abstract class ObjectLoader {
 	 *            stream to receive the complete copy of this object's data.
 	 *            Caller is responsible for flushing or closing this stream
 	 *            after this method returns.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object no longer exists.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed, or the stream cannot be
 	 *             written to.
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectReader.java

@@ -53,13 +53,13 @@ import java.util.Set;
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
-import org.eclipse.jgit.internal.storage.pack.ObjectReuseAsIs;
 
 /**
- * Reads an {@link ObjectDatabase} for a single thread.
+ * Reads an {@link org.eclipse.jgit.lib.ObjectDatabase} for a single thread.
  * <p>
  * Readers that can support efficient reuse of pack encoded objects should also
- * implement the companion interface {@link ObjectReuseAsIs}.
+ * implement the companion interface
+ * {@link org.eclipse.jgit.internal.storage.pack.ObjectReuseAsIs}.
  */
 public abstract class ObjectReader implements AutoCloseable {
 	/** Type hint indicating the caller doesn't know the type. */
@@ -95,7 +95,7 @@ public abstract class ObjectReader implements AutoCloseable {
 	 * @param objectId
 	 *            object identity that needs to be abbreviated.
 	 * @return SHA-1 abbreviation.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be read.
 	 */
 	public AbbreviatedObjectId abbreviate(AnyObjectId objectId)
@@ -122,7 +122,7 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *            [2, {@value Constants#OBJECT_ID_STRING_LENGTH}].
 	 * @return SHA-1 abbreviation. If no matching objects exist in the
 	 *         repository, the abbreviation will match the minimum length.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be read.
 	 */
 	public AbbreviatedObjectId abbreviate(AnyObjectId objectId, int len)
@@ -174,7 +174,7 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *            abbreviated id to resolve to a complete identity. The
 	 *            abbreviation must have a length of at least 2.
 	 * @return candidates that begin with the abbreviated identity.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be read.
 	 */
 	public abstract Collection<ObjectId> resolve(AbbreviatedObjectId id)
@@ -186,7 +186,7 @@ public abstract class ObjectReader implements AutoCloseable {
 	 * @param objectId
 	 *            identity of the object to test for existence of.
 	 * @return true if the specified object is stored in this database.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public boolean has(AnyObjectId objectId) throws IOException {
@@ -200,13 +200,14 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *            identity of the object to test for existence of.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
-	 *            {@link Constants#OBJ_BLOB}; {@link #OBJ_ANY} if the object
-	 *            type is not known, or does not matter to the caller.
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB};
+	 *            {@link #OBJ_ANY} if the object type is not known, or does not
+	 *            matter to the caller.
 	 * @return true if the specified object is stored in this database.
 	 * @throws IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public boolean has(AnyObjectId objectId, int typeHint) throws IOException {
@@ -223,10 +224,11 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *
 	 * @param objectId
 	 *            identity of the object to open.
-	 * @return a {@link ObjectLoader} for accessing the object.
-	 * @throws MissingObjectException
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the
+	 *         object.
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open(AnyObjectId objectId)
@@ -241,15 +243,17 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *            identity of the object to open.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
-	 *            {@link Constants#OBJ_BLOB}; {@link #OBJ_ANY} if the object
-	 *            type is not known, or does not matter to the caller.
-	 * @return a {@link ObjectLoader} for accessing the object.
-	 * @throws MissingObjectException
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB};
+	 *            {@link #OBJ_ANY} if the object type is not known, or does not
+	 *            matter to the caller.
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the
+	 *         object.
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public abstract ObjectLoader open(AnyObjectId objectId, int typeHint)
@@ -260,15 +264,13 @@ public abstract class ObjectReader implements AutoCloseable {
 	 * Returns IDs for those commits which should be considered as shallow.
 	 *
 	 * @return IDs of shallow commits
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract Set<ObjectId> getShallowCommits() throws IOException;
 
 	/**
 	 * Asynchronous object opening.
 	 *
-	 * @param <T>
-	 *            type of identifier being supplied.
 	 * @param objectIds
 	 *            objects to open from the object store. The supplied collection
 	 *            must not be modified until the queue has finished.
@@ -335,15 +337,16 @@ public abstract class ObjectReader implements AutoCloseable {
 	 *            identity of the object to open.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
-	 *            {@link Constants#OBJ_BLOB}; {@link #OBJ_ANY} if the object
-	 *            type is not known, or does not matter to the caller.
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB};
+	 *            {@link #OBJ_ANY} if the object type is not known, or does not
+	 *            matter to the caller.
 	 * @return size of object in bytes.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	public long getObjectSize(AnyObjectId objectId, int typeHint)
@@ -355,8 +358,6 @@ public abstract class ObjectReader implements AutoCloseable {
 	/**
 	 * Asynchronous object size lookup.
 	 *
-	 * @param <T>
-	 *            type of identifier being supplied.
 	 * @param objectIds
 	 *            objects to get the size of from the object store. The supplied
 	 *            collection must not be modified until the queue has finished.
@@ -433,7 +434,7 @@ public abstract class ObjectReader implements AutoCloseable {
 	 * An index that can be used to speed up ObjectWalks.
 	 *
 	 * @return the index or null if one does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             when the index fails to load
 	 * @since 3.0
 	 */
@@ -442,9 +443,12 @@ public abstract class ObjectReader implements AutoCloseable {
 	}
 
 	/**
-	 * @return the {@link ObjectInserter} from which this reader was created
-	 *         using {@code inserter.newReader()}, or null if this reader was not
-	 *         created from an inserter.
+	 * Get the {@link org.eclipse.jgit.lib.ObjectInserter} from which this
+	 * reader was created using {@code inserter.newReader()}
+	 *
+	 * @return the {@link org.eclipse.jgit.lib.ObjectInserter} from which this
+	 *         reader was created using {@code inserter.newReader()}, or null if
+	 *         this reader was not created from an inserter.
 	 * @since 4.4
 	 */
 	@Nullable
@@ -453,6 +457,8 @@ public abstract class ObjectReader implements AutoCloseable {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Release any resources used by this reader.
 	 * <p>
 	 * A reader that has been released can be used again, but may need to be

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectStream.java

@@ -46,12 +46,22 @@ package org.eclipse.jgit.lib;
 import java.io.IOException;
 import java.io.InputStream;
 
-/** Stream of data coming from an object loaded by {@link ObjectLoader}. */
+/**
+ * Stream of data coming from an object loaded by {@link org.eclipse.jgit.lib.ObjectLoader}.
+ */
 public abstract class ObjectStream extends InputStream {
-	/** @return Git object type, see {@link Constants}. */
+	/**
+	 * Get Git object type, see {@link Constants}.
+	 *
+	 * @return Git object type, see {@link Constants}.
+	 */
 	public abstract int getType();
 
-	/** @return total size of object in bytes */
+	/**
+	 * Get total size of object in bytes
+	 *
+	 * @return total size of object in bytes
+	 */
 	public abstract long getSize();
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/lib/PersonIdent.java

@@ -65,6 +65,8 @@ public class PersonIdent implements Serializable {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Get timezone object for the given offset.
+	 *
 	 * @param tzOffset
 	 *            timezone offset as in {@link #getTimeZoneOffset()}.
 	 * @return time zone object for the given offset.
@@ -163,38 +165,45 @@ public class PersonIdent implements Serializable {
 	 * This new PersonIdent gets the info from the default committer as available
 	 * from the configuration.
 	 *
-	 * @param repo
+	 * @param repo a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public PersonIdent(final Repository repo) {
 		this(repo.getConfig().get(UserConfig.KEY));
 	}
 
 	/**
-	 * Copy a {@link PersonIdent}.
+	 * Copy a {@link org.eclipse.jgit.lib.PersonIdent}.
 	 *
 	 * @param pi
-	 *            Original {@link PersonIdent}
+	 *            Original {@link org.eclipse.jgit.lib.PersonIdent}
 	 */
 	public PersonIdent(final PersonIdent pi) {
 		this(pi.getName(), pi.getEmailAddress());
 	}
 
 	/**
-	 * Construct a new {@link PersonIdent} with current time.
+	 * Construct a new {@link org.eclipse.jgit.lib.PersonIdent} with current
+	 * time.
 	 *
 	 * @param aName
+	 *            a {@link java.lang.String} object.
 	 * @param aEmailAddress
+	 *            a {@link java.lang.String} object.
 	 */
 	public PersonIdent(final String aName, final String aEmailAddress) {
 		this(aName, aEmailAddress, SystemReader.getInstance().getCurrentTime());
 	}
 
 	/**
-	 * Construct a new {@link PersonIdent} with current time.
+	 * Construct a new {@link org.eclipse.jgit.lib.PersonIdent} with current
+	 * time.
 	 *
 	 * @param aName
+	 *            a {@link java.lang.String} object.
 	 * @param aEmailAddress
+	 *            a {@link java.lang.String} object.
 	 * @param when
+	 *            a {@link org.eclipse.jgit.util.time.ProposedTimestamp} object.
 	 * @since 4.6
 	 */
 	public PersonIdent(String aName, String aEmailAddress,
@@ -206,7 +215,7 @@ public class PersonIdent implements Serializable {
 	 * Copy a PersonIdent, but alter the clone's time stamp
 	 *
 	 * @param pi
-	 *            original {@link PersonIdent}
+	 *            original {@link org.eclipse.jgit.lib.PersonIdent}
 	 * @param when
 	 *            local time
 	 * @param tz
@@ -217,10 +226,11 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
-	 * Copy a {@link PersonIdent}, but alter the clone's time stamp
+	 * Copy a {@link org.eclipse.jgit.lib.PersonIdent}, but alter the clone's
+	 * time stamp
 	 *
 	 * @param pi
-	 *            original {@link PersonIdent}
+	 *            original {@link org.eclipse.jgit.lib.PersonIdent}
 	 * @param aWhen
 	 *            local time
 	 */
@@ -231,8 +241,8 @@ public class PersonIdent implements Serializable {
 	/**
 	 * Construct a PersonIdent from simple data
 	 *
-	 * @param aName
-	 * @param aEmailAddress
+	 * @param aName a {@link java.lang.String} object.
+	 * @param aEmailAddress a {@link java.lang.String} object.
 	 * @param aWhen
 	 *            local time stamp
 	 * @param aTZ
@@ -248,7 +258,7 @@ public class PersonIdent implements Serializable {
 	 * Copy a PersonIdent, but alter the clone's time stamp
 	 *
 	 * @param pi
-	 *            original {@link PersonIdent}
+	 *            original {@link org.eclipse.jgit.lib.PersonIdent}
 	 * @param aWhen
 	 *            local time stamp
 	 * @param aTZ
@@ -269,7 +279,7 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
-	 * Construct a {@link PersonIdent}.
+	 * Construct a {@link org.eclipse.jgit.lib.PersonIdent}.
 	 * <p>
 	 * Whitespace in the name and email is preserved for the lifetime of this
 	 * object, but are trimmed by {@link #toExternalString()}. This means that
@@ -277,7 +287,9 @@ public class PersonIdent implements Serializable {
 	 * equivalent instance.
 	 *
 	 * @param aName
+	 *            a {@link java.lang.String} object.
 	 * @param aEmailAddress
+	 *            a {@link java.lang.String} object.
 	 * @param aWhen
 	 *            local time stamp
 	 * @param aTZ
@@ -298,6 +310,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * Get name of person
+	 *
 	 * @return Name of person
 	 */
 	public String getName() {
@@ -305,6 +319,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * Get email address of person
+	 *
 	 * @return email address of person
 	 */
 	public String getEmailAddress() {
@@ -312,6 +328,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * Get timestamp
+	 *
 	 * @return timestamp
 	 */
 	public Date getWhen() {
@@ -319,6 +337,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * Get this person's declared time zone
+	 *
 	 * @return this person's declared time zone; null if time zone is unknown.
 	 */
 	public TimeZone getTimeZone() {
@@ -326,6 +346,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * Get this person's declared time zone as minutes east of UTC.
+	 *
 	 * @return this person's declared time zone as minutes east of UTC. If the
 	 *         timezone is to the west of UTC it is negative.
 	 */
@@ -334,6 +356,8 @@ public class PersonIdent implements Serializable {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Hashcode is based only on the email address and timestamp.
 	 */
 	@Override
@@ -344,6 +368,7 @@ public class PersonIdent implements Serializable {
 		return hc;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(final Object o) {
 		if (o instanceof PersonIdent) {
@@ -372,6 +397,7 @@ public class PersonIdent implements Serializable {
 		return r.toString();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@SuppressWarnings("nls")
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/ProgressMonitor.java

@@ -44,7 +44,9 @@
 
 package org.eclipse.jgit.lib;
 
-/** A progress reporting interface. */
+/**
+ * A progress reporting interface.
+ */
 public interface ProgressMonitor {
 	/** Constant indicating the total work units cannot be predicted. */
 	public static final int UNKNOWN = 0;
@@ -85,7 +87,9 @@ public interface ProgressMonitor {
 	 */
 	void update(int completed);
 
-	/** Finish the current task, so the next can begin. */
+	/**
+	 * Finish the current task, so the next can begin.
+	 */
 	void endTask();
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoFile.java

@@ -67,7 +67,10 @@ public class RebaseTodoFile {
 	private Repository repo;
 
 	/**
+	 * Constructor for RebaseTodoFile.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public RebaseTodoFile(Repository repo) {
 		this.repo = repo;
@@ -84,7 +87,7 @@ public class RebaseTodoFile {
 	 * @param includeComments
 	 *            <code>true</code> if also comments should be reported
 	 * @return the list of steps
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public List<RebaseTodoLine> readRebaseTodo(String path,
 			boolean includeComments) throws IOException {
@@ -214,7 +217,7 @@ public class RebaseTodoFile {
 	 *            the steps to be written
 	 * @param append
 	 *            whether to append to an existing file or to write a new file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeRebaseTodoFile(String path, List<RebaseTodoLine> steps,
 			boolean append) throws IOException {

org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoLine.java

@@ -142,8 +142,11 @@ public class RebaseTodoLine {
 	 * Create a new non-comment line
 	 *
 	 * @param action
+	 *            a {@link org.eclipse.jgit.lib.RebaseTodoLine.Action} object.
 	 * @param commit
+	 *            a {@link org.eclipse.jgit.lib.AbbreviatedObjectId} object.
 	 * @param shortMessage
+	 *            a {@link java.lang.String} object.
 	 */
 	public RebaseTodoLine(Action action, AbbreviatedObjectId commit,
 			String shortMessage) {
@@ -154,6 +157,8 @@ public class RebaseTodoLine {
 	}
 
 	/**
+	 * Get rebase action type
+	 *
 	 * @return rebase action type
 	 */
 	public Action getAction() {
@@ -167,7 +172,8 @@ public class RebaseTodoLine {
 	 * non-comment.
 	 *
 	 * @param newAction
-	 * @throws IllegalTodoFileModification
+	 *            a {@link org.eclipse.jgit.lib.RebaseTodoLine.Action} object.
+	 * @throws org.eclipse.jgit.errors.IllegalTodoFileModification
 	 *             on attempt to set a non-comment action on a line which was a
 	 *             comment line before.
 	 */
@@ -193,7 +199,7 @@ public class RebaseTodoLine {
 	/**
 	 * <p>
 	 * Set a comment for this line that is used if this line's
-	 * {@link RebaseTodoLine#action} is a {@link Action#COMMENT}
+	 * {@link org.eclipse.jgit.lib.RebaseTodoLine#action} is a {@link org.eclipse.jgit.lib.RebaseTodoLine.Action#COMMENT}
 	 * </p>
 	 * It's allowed to unset the comment by calling
 	 * <code>setComment(null)</code> <br>
@@ -230,6 +236,8 @@ public class RebaseTodoLine {
 	}
 
 	/**
+	 * Get abbreviated commit SHA-1 of commit that action will be performed on
+	 *
 	 * @return abbreviated commit SHA-1 of commit that action will be performed
 	 *         on
 	 */
@@ -238,6 +246,9 @@ public class RebaseTodoLine {
 	}
 
 	/**
+	 * Get the first line of the commit message of the commit the action will be
+	 * performed on.
+	 *
 	 * @return the first line of the commit message of the commit the action
 	 *         will be performed on.
 	 */
@@ -246,13 +257,18 @@ public class RebaseTodoLine {
 	}
 
 	/**
+	 * Set short message
+	 *
 	 * @param shortMessage
+	 *            a short message.
 	 */
 	public void setShortMessage(String shortMessage) {
 		this.shortMessage = shortMessage;
 	}
 
 	/**
+	 * Get a comment
+	 *
 	 * @return a comment. If the line is a comment line then the comment is
 	 *         returned. Lines starting with # or blank lines or lines
 	 *         containing only spaces and tabs are considered as comment lines.
@@ -262,6 +278,7 @@ public class RebaseTodoLine {
 		return comment;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/Ref.java

@@ -47,7 +47,8 @@ import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 
 /**
- * Pairing of a name and the {@link ObjectId} it currently has.
+ * Pairing of a name and the {@link org.eclipse.jgit.lib.ObjectId} it currently
+ * has.
  * <p>
  * A ref in Git is (more or less) a variable that holds a single object
  * identifier. The object identifier can be any valid Git object (blob, tree,
@@ -135,9 +136,10 @@ public interface Ref {
 	/**
 	 * Test if this reference is a symbolic reference.
 	 * <p>
-	 * A symbolic reference does not have its own {@link ObjectId} value, but
-	 * instead points to another {@code Ref} in the same database and always
-	 * uses that other reference's value as its own.
+	 * A symbolic reference does not have its own
+	 * {@link org.eclipse.jgit.lib.ObjectId} value, but instead points to
+	 * another {@code Ref} in the same database and always uses that other
+	 * reference's value as its own.
 	 *
 	 * @return true if this is a symbolic reference; false if this reference
 	 *         contains its own ObjectId.
@@ -199,7 +201,9 @@ public interface Ref {
 	public abstract ObjectId getPeeledObjectId();
 
 	/**
-	 * @return whether the Ref represents a peeled tag
+	 * Whether the Ref represents a peeled tag.
+	 *
+	 * @return whether the Ref represents a peeled tag.
 	 */
 	public abstract boolean isPeeled();
 

org.eclipse.jgit/src/org/eclipse/jgit/lib/RefComparator.java

@@ -60,6 +60,7 @@ public class RefComparator implements Comparator<Ref> {
 	/** Singleton instance of RefComparator */
 	public static final RefComparator INSTANCE = new RefComparator();
 
+	/** {@inheritDoc} */
 	@Override
 	public int compare(final Ref o1, final Ref o2) {
 		return compareTo(o1, o2);

org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java

@@ -55,11 +55,13 @@ import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 
 /**
- * Abstraction of name to {@link ObjectId} mapping.
+ * Abstraction of name to {@link org.eclipse.jgit.lib.ObjectId} mapping.
  * <p>
- * A reference database stores a mapping of reference names to {@link ObjectId}.
- * Every {@link Repository} has a single reference database, mapping names to
- * the tips of the object graph contained by the {@link ObjectDatabase}.
+ * A reference database stores a mapping of reference names to
+ * {@link org.eclipse.jgit.lib.ObjectId}. Every
+ * {@link org.eclipse.jgit.lib.Repository} has a single reference database,
+ * mapping names to the tips of the object graph contained by the
+ * {@link org.eclipse.jgit.lib.ObjectDatabase}.
  */
 public abstract class RefDatabase {
 	/**
@@ -93,12 +95,14 @@ public abstract class RefDatabase {
 	/**
 	 * Initialize a new reference database at this location.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database could not be created.
 	 */
 	public abstract void create() throws IOException;
 
-	/** Close any resources held by this database. */
+	/**
+	 * Close any resources held by this database.
+	 */
 	public abstract void close();
 
 	/**
@@ -118,7 +122,7 @@ public abstract class RefDatabase {
 	 *            proposed name.
 	 * @return true if the name overlaps with an existing reference; false if
 	 *         using this name right now would be safe.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database could not be read to check for conflicts.
 	 * @see #getConflictingNames(String)
 	 */
@@ -133,7 +137,7 @@ public abstract class RefDatabase {
 	 * @return a collection of full names of existing refs which would conflict
 	 *         with the passed ref name; empty collection when there are no
 	 *         conflicts
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 2.3
 	 * @see #isNameConflicting(String)
 	 */
@@ -167,12 +171,13 @@ public abstract class RefDatabase {
 	 *            the name of the reference.
 	 * @param detach
 	 *            if {@code true} and {@code name} is currently a
-	 *            {@link SymbolicRef}, the update will replace it with an
-	 *            {@link ObjectIdRef}. Otherwise, the update will recursively
-	 *            traverse {@link SymbolicRef}s and operate on the leaf
-	 *            {@link ObjectIdRef}.
+	 *            {@link org.eclipse.jgit.lib.SymbolicRef}, the update will
+	 *            replace it with an {@link org.eclipse.jgit.lib.ObjectIdRef}.
+	 *            Otherwise, the update will recursively traverse
+	 *            {@link org.eclipse.jgit.lib.SymbolicRef}s and operate on the
+	 *            leaf {@link org.eclipse.jgit.lib.ObjectIdRef}.
 	 * @return a new update for the requested name; never null.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 */
 	@NonNull
@@ -187,7 +192,7 @@ public abstract class RefDatabase {
 	 * @param toName
 	 *            name of reference to rename to
 	 * @return an update command that knows how to rename a branch to another.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 */
 	@NonNull
@@ -210,20 +215,21 @@ public abstract class RefDatabase {
 	 * Whether the database is capable of performing batch updates as atomic
 	 * transactions.
 	 * <p>
-	 * If true, by default {@link BatchRefUpdate} instances will perform updates
-	 * atomically, meaning either all updates will succeed, or all updates will
-	 * fail. It is still possible to turn off this behavior on a per-batch basis
-	 * by calling {@code update.setAtomic(false)}.
+	 * If true, by default {@link org.eclipse.jgit.lib.BatchRefUpdate} instances
+	 * will perform updates atomically, meaning either all updates will succeed,
+	 * or all updates will fail. It is still possible to turn off this behavior
+	 * on a per-batch basis by calling {@code update.setAtomic(false)}.
 	 * <p>
-	 * If false, {@link BatchRefUpdate} instances will never perform updates
-	 * atomically, and calling {@code update.setAtomic(true)} will cause the
-	 * entire batch to fail with {@code REJECTED_OTHER_REASON}.
+	 * If false, {@link org.eclipse.jgit.lib.BatchRefUpdate} instances will
+	 * never perform updates atomically, and calling
+	 * {@code update.setAtomic(true)} will cause the entire batch to fail with
+	 * {@code REJECTED_OTHER_REASON}.
 	 * <p>
 	 * This definition of atomicity is stronger than what is provided by
 	 * {@link org.eclipse.jgit.transport.ReceivePack}. {@code ReceivePack} will
 	 * attempt to reject all commands if it knows in advance some commands may
-	 * fail, even if the storage layer does not support atomic transactions. Here,
-	 * atomicity applies even in the case of unforeseeable errors.
+	 * fail, even if the storage layer does not support atomic transactions.
+	 * Here, atomicity applies even in the case of unforeseeable errors.
 	 *
 	 * @return whether transactions are atomic by default.
 	 * @since 3.6
@@ -246,7 +252,7 @@ public abstract class RefDatabase {
 	 *            the name of the reference. May be a short name which must be
 	 *            searched for using the standard {@link #SEARCH_PATH}.
 	 * @return the reference (if it exists); else {@code null}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 */
 	@Nullable
@@ -261,7 +267,7 @@ public abstract class RefDatabase {
 	 * @param name
 	 *             the unabbreviated name of the reference.
 	 * @return the reference (if it exists); else {@code null}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 * @since 4.1
 	 */
@@ -285,7 +291,7 @@ public abstract class RefDatabase {
 	 *             the unabbreviated names of references to look up.
 	 * @return modifiable map describing any refs that exist among the ref
 	 *         ref names supplied. The map can be an unsorted map.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 * @since 4.1
 	 */
@@ -310,7 +316,7 @@ public abstract class RefDatabase {
 	 * @param refs
 	 *             the unabbreviated names of references to look up.
 	 * @return the first named reference that exists (if any); else {@code null}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 * @since 4.1
 	 */
@@ -335,7 +341,7 @@ public abstract class RefDatabase {
 	 * @return modifiable map that is a complete snapshot of the current
 	 *         reference namespace, with {@code prefix} removed from the start
 	 *         of each key. The map can be an unsorted map.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 */
 	@NonNull
@@ -350,7 +356,7 @@ public abstract class RefDatabase {
 	 * and {@link #exactRef(String)}.
 	 *
 	 * @return a list of additional refs
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
 	 */
 	@NonNull
@@ -360,10 +366,11 @@ public abstract class RefDatabase {
 	 * Peel a possibly unpeeled reference by traversing the annotated tags.
 	 * <p>
 	 * If the reference cannot be peeled (as it does not refer to an annotated
-	 * tag) the peeled id stays null, but {@link Ref#isPeeled()} will be true.
+	 * tag) the peeled id stays null, but
+	 * {@link org.eclipse.jgit.lib.Ref#isPeeled()} will be true.
 	 * <p>
-	 * Implementors should check {@link Ref#isPeeled()} before performing any
-	 * additional work effort.
+	 * Implementors should check {@link org.eclipse.jgit.lib.Ref#isPeeled()}
+	 * before performing any additional work effort.
 	 *
 	 * @param ref
 	 *            The reference to peel
@@ -371,7 +378,7 @@ public abstract class RefDatabase {
 	 *         Ref object representing the same data as Ref, but isPeeled() will
 	 *         be true and getPeeledObjectId() will contain the peeled object
 	 *         (or {@code null}).
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the reference space or object space cannot be accessed.
 	 */
 	@NonNull

org.eclipse.jgit/src/org/eclipse/jgit/lib/RefRename.java

@@ -86,7 +86,11 @@ public abstract class RefRename {
 				+ Repository.shortenRefName(destination.getName()));
 	}
 
-	/** @return identity of the user making the change in the reflog. */
+	/**
+	 * Get identity of the user making the change in the reflog.
+	 *
+	 * @return identity of the user making the change in the reflog.
+	 */
 	public PersonIdent getRefLogIdent() {
 		return destination.getRefLogIdent();
 	}
@@ -130,12 +134,16 @@ public abstract class RefRename {
 			destination.setRefLogMessage(msg, false);
 	}
 
-	/** Don't record this rename in the ref's associated reflog. */
+	/**
+	 * Don't record this rename in the ref's associated reflog.
+	 */
 	public void disableRefLog() {
 		destination.setRefLogMessage("", false); //$NON-NLS-1$
 	}
 
 	/**
+	 * Get result of rename operation
+	 *
 	 * @return result of rename operation
 	 */
 	public Result getResult() {
@@ -143,8 +151,10 @@ public abstract class RefRename {
 	}
 
 	/**
+	 * Rename
+	 *
 	 * @return the result of the new ref update
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public Result rename() throws IOException {
 		try {
@@ -157,15 +167,20 @@ public abstract class RefRename {
 	}
 
 	/**
+	 * Do the actual rename
+	 *
 	 * @return the result of the rename operation.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected abstract Result doRename() throws IOException;
 
 	/**
+	 * Whether the {@code Constants#HEAD} reference needs to be linked to the
+	 * new destination name.
+	 *
 	 * @return true if the {@code Constants#HEAD} reference needs to be linked
 	 *         to the new destination name.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the current value of {@code HEAD} cannot be read.
 	 */
 	protected boolean needToUpdateHEAD() throws IOException {

org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java

@@ -233,10 +233,18 @@ public abstract class RefUpdate {
 		refLogMessage = ""; //$NON-NLS-1$
 	}
 
-	/** @return the reference database this update modifies. */
+	/**
+	 * Get the reference database this update modifies.
+	 *
+	 * @return the reference database this update modifies.
+	 */
 	protected abstract RefDatabase getRefDatabase();
 
-	/** @return the repository storing the database's objects. */
+	/**
+	 * Get the repository storing the database's objects.
+	 *
+	 * @return the repository storing the database's objects.
+	 */
 	protected abstract Repository getRepository();
 
 	/**
@@ -251,33 +259,44 @@ public abstract class RefUpdate {
 	 *            current reference.
 	 * @return true if the lock was acquired and the reference is likely
 	 *         protected from concurrent modification; false if it failed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the lock couldn't be taken due to an unexpected storage
 	 *             failure, and not because of a concurrent update.
 	 */
 	protected abstract boolean tryLock(boolean deref) throws IOException;
 
-	/** Releases the lock taken by {@link #tryLock} if it succeeded. */
+	/**
+	 * Releases the lock taken by {@link #tryLock} if it succeeded.
+	 */
 	protected abstract void unlock();
 
 	/**
+	 * Do update
+	 *
 	 * @param desiredResult
+	 *            a {@link org.eclipse.jgit.lib.RefUpdate.Result} object.
 	 * @return {@code result}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected abstract Result doUpdate(Result desiredResult) throws IOException;
 
 	/**
+	 * Do delete
+	 *
 	 * @param desiredResult
+	 *            a {@link org.eclipse.jgit.lib.RefUpdate.Result} object.
 	 * @return {@code result}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected abstract Result doDelete(Result desiredResult) throws IOException;
 
 	/**
+	 * Do link
+	 *
 	 * @param target
-	 * @return {@link Result#NEW} on success.
-	 * @throws IOException
+	 *            a {@link java.lang.String} object.
+	 * @return {@link org.eclipse.jgit.lib.RefUpdate.Result#NEW} on success.
+	 * @throws java.io.IOException
 	 */
 	protected abstract Result doLink(String target) throws IOException;
 
@@ -290,7 +309,11 @@ public abstract class RefUpdate {
 		return getRef().getName();
 	}
 
-	/** @return the reference this update will create or modify. */
+	/**
+	 * Get the reference this update will create or modify.
+	 *
+	 * @return the reference this update will create or modify.
+	 */
 	public Ref getRef() {
 		return ref;
 	}
@@ -332,21 +355,27 @@ public abstract class RefUpdate {
 	}
 
 	/**
+	 * Get the expected value of the ref after the lock is taken, but before
+	 * update occurs.
+	 *
 	 * @return the expected value of the ref after the lock is taken, but before
 	 *         update occurs. Null to avoid the compare and swap test. Use
-	 *         {@link ObjectId#zeroId()} to indicate expectation of a
-	 *         non-existant ref.
+	 *         {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate
+	 *         expectation of a non-existant ref.
 	 */
 	public ObjectId getExpectedOldObjectId() {
 		return expValue;
 	}
 
 	/**
+	 * Set the expected value of the ref after the lock is taken, but before
+	 * update occurs.
+	 *
 	 * @param id
 	 *            the expected value of the ref after the lock is taken, but
 	 *            before update occurs. Null to avoid the compare and swap test.
-	 *            Use {@link ObjectId#zeroId()} to indicate expectation of a
-	 *            non-existant ref.
+	 *            Use {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate
+	 *            expectation of a non-existant ref.
 	 */
 	public void setExpectedOldObjectId(final AnyObjectId id) {
 		expValue = id != null ? id.toObjectId() : null;
@@ -371,7 +400,11 @@ public abstract class RefUpdate {
 		force = b;
 	}
 
-	/** @return identity of the user making the change in the reflog. */
+	/**
+	 * Get identity of the user making the change in the reflog.
+	 *
+	 * @return identity of the user making the change in the reflog.
+	 */
 	public PersonIdent getRefLogIdent() {
 		return refLogIdent;
 	}
@@ -402,7 +435,11 @@ public abstract class RefUpdate {
 		return refLogMessage;
 	}
 
-	/** @return {@code true} if the ref log message should show the result. */
+	/**
+	 * Whether the ref log message should show the result.
+	 *
+	 * @return {@code true} if the ref log message should show the result.
+	 */
 	protected boolean isRefLogIncludingResult() {
 		return refLogIncludeResult;
 	}
@@ -436,7 +473,9 @@ public abstract class RefUpdate {
 		}
 	}
 
-	/** Don't record this update in the ref's associated reflog. */
+	/**
+	 * Don't record this update in the ref's associated reflog.
+	 */
 	public void disableRefLog() {
 		refLogMessage = null;
 		refLogIncludeResult = false;
@@ -535,7 +574,7 @@ public abstract class RefUpdate {
 	 * the merge test is performed.
 	 *
 	 * @return the result status of the update.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an unexpected IO error occurred while writing changes.
 	 */
 	public Result forceUpdate() throws IOException {
@@ -555,7 +594,7 @@ public abstract class RefUpdate {
 	 * </pre>
 	 *
 	 * @return the result status of the update.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an unexpected IO error occurred while writing changes.
 	 */
 	public Result update() throws IOException {
@@ -573,7 +612,7 @@ public abstract class RefUpdate {
 	 *            a RevWalk instance this update command can borrow to perform
 	 *            the merge test. The walk will be reset to perform the test.
 	 * @return the result status of the update.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an unexpected IO error occurred while writing changes.
 	 */
 	public Result update(final RevWalk walk) throws IOException {
@@ -603,7 +642,7 @@ public abstract class RefUpdate {
 	 * </pre>
 	 *
 	 * @return the result status of the delete.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public Result delete() throws IOException {
 		try (RevWalk rw = new RevWalk(getRepository())) {
@@ -618,7 +657,7 @@ public abstract class RefUpdate {
 	 *            a RevWalk instance this delete command can borrow to perform
 	 *            the merge test. The walk will be reset to perform the test.
 	 * @return the result status of the delete.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public Result delete(final RevWalk walk) throws IOException {
 		final String myName = detachingSymbolicRef
@@ -656,8 +695,9 @@ public abstract class RefUpdate {
 	 * @param target
 	 *            name of the new target for this reference. The new target name
 	 *            must be absolute, so it must begin with {@code refs/}.
-	 * @return {@link Result#NEW} or {@link Result#FORCED} on success.
-	 * @throws IOException
+	 * @return {@link org.eclipse.jgit.lib.RefUpdate.Result#NEW} or
+	 *         {@link org.eclipse.jgit.lib.RefUpdate.Result#FORCED} on success.
+	 * @throws java.io.IOException
 	 */
 	public Result link(String target) throws IOException {
 		if (!target.startsWith(Constants.R_REFS))
@@ -751,6 +791,7 @@ public abstract class RefUpdate {
 	 * are checked explicitly.
 	 *
 	 * @param check
+	 *            whether to enable the check for conflicting ref names.
 	 * @since 3.0
 	 */
 	public void setCheckConflicting(boolean check) {

org.eclipse.jgit/src/org/eclipse/jgit/lib/RefWriter.java

@@ -56,8 +56,8 @@ import org.eclipse.jgit.util.RefList;
 import org.eclipse.jgit.util.RefMap;
 
 /**
- * Writes out refs to the {@link Constants#INFO_REFS} and
- * {@link Constants#PACKED_REFS} files.
+ * Writes out refs to the {@link org.eclipse.jgit.lib.Constants#INFO_REFS} and
+ * {@link org.eclipse.jgit.lib.Constants#PACKED_REFS} files.
  *
  * This class is abstract as the writing of the files must be handled by the
  * caller. This is because it is used by transport classes as well.
@@ -67,6 +67,8 @@ public abstract class RefWriter {
 	private final Collection<Ref> refs;
 
 	/**
+	 * <p>Constructor for RefWriter.</p>
+	 *
 	 * @param refs
 	 *            the complete set of references. This should have been computed
 	 *            by applying updates to the advertised refs already discovered.
@@ -76,6 +78,8 @@ public abstract class RefWriter {
 	}
 
 	/**
+	 * <p>Constructor for RefWriter.</p>
+	 *
 	 * @param refs
 	 *            the complete set of references. This should have been computed
 	 *            by applying updates to the advertised refs already discovered.
@@ -88,6 +92,8 @@ public abstract class RefWriter {
 	}
 
 	/**
+	 * <p>Constructor for RefWriter.</p>
+	 *
 	 * @param refs
 	 *            the complete set of references. This should have been computed
 	 *            by applying updates to the advertised refs already discovered.
@@ -97,13 +103,13 @@ public abstract class RefWriter {
 	}
 
 	/**
-	 * Rebuild the {@link Constants#INFO_REFS}.
+	 * Rebuild the {@link org.eclipse.jgit.lib.Constants#INFO_REFS}.
 	 * <p>
-	 * This method rebuilds the contents of the {@link Constants#INFO_REFS} file
-	 * to match the passed list of references.
-	 *
+	 * This method rebuilds the contents of the
+	 * {@link org.eclipse.jgit.lib.Constants#INFO_REFS} file to match the passed
+	 * list of references.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             writing is not supported, or attempting to write the file
 	 *             failed, possibly due to permissions or remote disk full, etc.
 	 */
@@ -142,13 +148,14 @@ public abstract class RefWriter {
 	}
 
 	/**
-	 * Rebuild the {@link Constants#PACKED_REFS} file.
+	 * Rebuild the {@link org.eclipse.jgit.lib.Constants#PACKED_REFS} file.
 	 * <p>
-	 * This method rebuilds the contents of the {@link Constants#PACKED_REFS}
-	 * file to match the passed list of references, including only those refs
-	 * that have a storage type of {@link Ref.Storage#PACKED}.
+	 * This method rebuilds the contents of the
+	 * {@link org.eclipse.jgit.lib.Constants#PACKED_REFS} file to match the
+	 * passed list of references, including only those refs that have a storage
+	 * type of {@link org.eclipse.jgit.lib.Ref.Storage#PACKED}.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             writing is not supported, or attempting to write the file
 	 *             failed, possibly due to permissions or remote disk full, etc.
 	 */
@@ -203,7 +210,7 @@ public abstract class RefWriter {
 	 *            path to ref file.
 	 * @param content
 	 *            byte content of file to be written.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected abstract void writeFile(String file, byte[] content)
 			throws IOException;

org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogEntry.java

@@ -83,28 +83,39 @@ public interface ReflogEntry {
 	public static final String PREFIX_FORCED_UPDATE = "forced-update"; //$NON-NLS-1$
 
 	/**
+	 * Get the commit id before the change
+	 *
 	 * @return the commit id before the change
 	 */
 	public abstract ObjectId getOldId();
 
 	/**
+	 * Get the commit id after the change
+	 *
 	 * @return the commit id after the change
 	 */
 	public abstract ObjectId getNewId();
 
 	/**
+	 * Get user performing the change
+	 *
 	 * @return user performing the change
 	 */
 	public abstract PersonIdent getWho();
 
 	/**
+	 * Get textual description of the change
+	 *
 	 * @return textual description of the change
 	 */
 	public abstract String getComment();
 
 	/**
-	 * @return a {@link CheckoutEntry} with parsed information about a branch
-	 *         switch, or null if the entry is not a checkout
+	 * Parse checkout
+	 *
+	 * @return a {@link org.eclipse.jgit.lib.CheckoutEntry} with parsed
+	 *         information about a branch switch, or null if the entry is not a
+	 *         checkout
 	 */
 	public abstract CheckoutEntry parseCheckout();
 

org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogReader.java

@@ -57,13 +57,15 @@ public interface ReflogReader {
 	 * Get the last entry in the reflog
 	 *
 	 * @return the latest reflog entry, or null if no log
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract ReflogEntry getLastEntry() throws IOException;
 
 	/**
+	 * Get all reflog entries in reverse order
+	 *
 	 * @return all reflog entries in reverse order
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract List<ReflogEntry> getReverseEntries() throws IOException;
 
@@ -71,17 +73,19 @@ public interface ReflogReader {
 	 * Get specific entry in the reflog relative to the last entry which is
 	 * considered entry zero.
 	 *
-	 * @param number
+	 * @param number a int.
 	 * @return reflog entry or null if not found
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract ReflogEntry getReverseEntry(int number) throws IOException;
 
 	/**
+	 * Get all reflog entries in reverse order
+	 *
 	 * @param max
 	 *            max number of entries to read
 	 * @return all reflog entries in reverse order
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract List<ReflogEntry> getReverseEntries(int max)
 			throws IOException;

org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java

@@ -83,7 +83,6 @@ import org.eclipse.jgit.events.IndexChangedListener;
 import org.eclipse.jgit.events.ListenerList;
 import org.eclipse.jgit.events.RepositoryEvent;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.internal.storage.file.GC;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
@@ -106,9 +105,9 @@ import org.slf4j.LoggerFactory;
  * A repository holds all objects and refs used for managing source code (could
  * be any type of file, but source code is what SCM's are typically used for).
  * <p>
- * The thread-safety of a {@link Repository} very much depends on the concrete
- * implementation. Applications working with a generic {@code Repository} type
- * must not assume the instance is thread-safe.
+ * The thread-safety of a {@link org.eclipse.jgit.lib.Repository} very much
+ * depends on the concrete implementation. Applications working with a generic
+ * {@code Repository} type must not assume the instance is thread-safe.
  * <ul>
  * <li>{@code FileRepository} is thread-safe.
  * <li>{@code DfsRepository} thread-safety is determined by its subclass.
@@ -129,7 +128,11 @@ public abstract class Repository implements AutoCloseable {
 					"(^|/)(aux|com[1-9]|con|lpt[1-9]|nul|prn)(\\.[^/]*)?", //$NON-NLS-1$
 					Pattern.CASE_INSENSITIVE);
 
-	/** @return the global listener list observing all events in this JVM. */
+	/**
+	 * Get the global listener list observing all events in this JVM.
+	 *
+	 * @return the global listener list observing all events in this JVM.
+	 */
 	public static ListenerList getGlobalListenerList() {
 		return globalListeners;
 	}
@@ -166,7 +169,11 @@ public abstract class Repository implements AutoCloseable {
 		indexFile = options.getIndexFile();
 	}
 
-	/** @return listeners observing only events on this repository. */
+	/**
+	 * Get listeners observing only events on this repository.
+	 *
+	 * @return listeners observing only events on this repository.
+	 */
 	@NonNull
 	public ListenerList getListenerList() {
 		return myListeners;
@@ -193,7 +200,7 @@ public abstract class Repository implements AutoCloseable {
 	 * Repository with working tree is created using this method. This method is
 	 * the same as {@code create(false)}.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @see #create(boolean)
 	 */
 	public void create() throws IOException {
@@ -207,12 +214,14 @@ public abstract class Repository implements AutoCloseable {
 	 * @param bare
 	 *            if true, a bare repository (a repository without a working
 	 *            directory) is created.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             in case of IO problem
 	 */
 	public abstract void create(boolean bare) throws IOException;
 
 	/**
+	 * Get local metadata directory
+	 *
 	 * @return local metadata directory; {@code null} if repository isn't local.
 	 */
 	/*
@@ -227,44 +236,64 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get the object database which stores this repository's data.
+	 *
 	 * @return the object database which stores this repository's data.
 	 */
 	@NonNull
 	public abstract ObjectDatabase getObjectDatabase();
 
-	/** @return a new inserter to create objects in {@link #getObjectDatabase()} */
+	/**
+	 * Create a new inserter to create objects in {@link #getObjectDatabase()}.
+	 *
+	 * @return a new inserter to create objects in {@link #getObjectDatabase()}.
+	 */
 	@NonNull
 	public ObjectInserter newObjectInserter() {
 		return getObjectDatabase().newInserter();
 	}
 
-	/** @return a new reader to read objects from {@link #getObjectDatabase()} */
+	/**
+	 * Create a new reader to read objects from {@link #getObjectDatabase()}.
+	 *
+	 * @return a new reader to read objects from {@link #getObjectDatabase()}.
+	 */
 	@NonNull
 	public ObjectReader newObjectReader() {
 		return getObjectDatabase().newReader();
 	}
 
-	/** @return the reference database which stores the reference namespace. */
+	/**
+	 * Get the reference database which stores the reference namespace.
+	 *
+	 * @return the reference database which stores the reference namespace.
+	 */
 	@NonNull
 	public abstract RefDatabase getRefDatabase();
 
 	/**
-	 * @return the configuration of this repository
+	 * Get the configuration of this repository.
+	 *
+	 * @return the configuration of this repository.
 	 */
 	@NonNull
 	public abstract StoredConfig getConfig();
 
 	/**
-	 * @return a new {@link AttributesNodeProvider}. This
-	 *         {@link AttributesNodeProvider} is lazy loaded only once. It means
-	 *         that it will not be updated after loading. Prefer creating new
-	 *         instance for each use.
+	 * Create a new {@link org.eclipse.jgit.attributes.AttributesNodeProvider}.
+	 *
+	 * @return a new {@link org.eclipse.jgit.attributes.AttributesNodeProvider}.
+	 *         This {@link org.eclipse.jgit.attributes.AttributesNodeProvider}
+	 *         is lazy loaded only once. It means that it will not be updated
+	 *         after loading. Prefer creating new instance for each use.
 	 * @since 4.2
 	 */
 	@NonNull
 	public abstract AttributesNodeProvider createAttributesNodeProvider();
 
 	/**
+	 * Get the used file system abstraction.
+	 *
 	 * @return the used file system abstraction, or or {@code null} if
 	 *         repository isn't local.
 	 */
@@ -280,7 +309,11 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Whether the specified object is stored in this repo or any of the known
+	 * shared repositories.
+	 *
 	 * @param objectId
+	 *            a {@link org.eclipse.jgit.lib.AnyObjectId} object.
 	 * @return true if the specified object is stored in this repo or any of the
 	 *         known shared repositories.
 	 */
@@ -301,10 +334,11 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @param objectId
 	 *            identity of the object to open.
-	 * @return a {@link ObjectLoader} for accessing the object.
-	 * @throws MissingObjectException
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the
+	 *         object.
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	@NonNull
@@ -323,16 +357,17 @@ public abstract class Repository implements AutoCloseable {
 	 *            identity of the object to open.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
-	 *            {@link Constants#OBJ_BLOB}; {@link ObjectReader#OBJ_ANY} if
-	 *            the object type is not known, or does not matter to the
-	 *            caller.
-	 * @return a {@link ObjectLoader} for accessing the object.
-	 * @throws MissingObjectException
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB};
+	 *            {@link org.eclipse.jgit.lib.ObjectReader#OBJ_ANY} if the
+	 *            object type is not known, or does not matter to the caller.
+	 * @return a {@link org.eclipse.jgit.lib.ObjectLoader} for accessing the
+	 *         object.
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object does not exist.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object store cannot be accessed.
 	 */
 	@NonNull
@@ -350,7 +385,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @return an update command. The caller must finish populating this command
 	 *         and then invoke one of the update methods to actually make a
 	 *         change.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a symbolic ref was passed in and could not be resolved back
 	 *             to the base ref, as the symbolic ref could not be read.
 	 */
@@ -369,7 +404,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @return an update command. The caller must finish populating this command
 	 *         and then invoke one of the update methods to actually make a
 	 *         change.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a symbolic ref was passed in and could not be resolved back
 	 *             to the base ref, as the symbolic ref could not be read.
 	 */
@@ -386,9 +421,8 @@ public abstract class Repository implements AutoCloseable {
 	 * @param toRef
 	 *            name of ref to rename to
 	 * @return an update command that knows how to rename a branch to another.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the rename could not be performed.
-	 *
 	 */
 	@NonNull
 	public RefRename renameRef(final String fromRef, final String toRef) throws IOException {
@@ -432,17 +466,17 @@ public abstract class Repository implements AutoCloseable {
 	 *            A git object references expression
 	 * @return an ObjectId or {@code null} if revstr can't be resolved to any
 	 *         ObjectId
-	 * @throws AmbiguousObjectException
+	 * @throws org.eclipse.jgit.errors.AmbiguousObjectException
 	 *             {@code revstr} contains an abbreviated ObjectId and this
 	 *             repository contains more than one object which match to the
 	 *             input abbreviation.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             the id parsed does not meet the type required to finish
 	 *             applying the operators in the expression.
-	 * @throws RevisionSyntaxException
+	 * @throws org.eclipse.jgit.errors.RevisionSyntaxException
 	 *             the expression is not supported by this implementation, or
 	 *             does not meet the standard syntax.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             on serious errors
 	 */
 	@Nullable
@@ -466,11 +500,11 @@ public abstract class Repository implements AutoCloseable {
 	 * Thus this method can be used to process an expression to a method that
 	 * expects a branch or revision id.
 	 *
-	 * @param revstr
+	 * @param revstr a {@link java.lang.String} object.
 	 * @return object id or ref name from resolved expression or {@code null} if
 	 *         given expression cannot be resolved
-	 * @throws AmbiguousObjectException
-	 * @throws IOException
+	 * @throws org.eclipse.jgit.errors.AmbiguousObjectException
+	 * @throws java.io.IOException
 	 */
 	@Nullable
 	public String simplify(final String revstr)
@@ -889,12 +923,18 @@ public abstract class Repository implements AutoCloseable {
 		}
 	}
 
-	/** Increment the use counter by one, requiring a matched {@link #close()}. */
+	/**
+	 * Increment the use counter by one, requiring a matched {@link #close()}.
+	 */
 	public void incrementOpen() {
 		useCnt.incrementAndGet();
 	}
 
-	/** Decrement the use count, and maybe close resources. */
+	/**
+	 * {@inheritDoc}
+	 * <p>
+	 * Decrement the use count, and maybe close resources.
+	 */
 	@Override
 	public void close() {
 		int newCount = useCnt.decrementAndGet();
@@ -930,6 +970,7 @@ public abstract class Repository implements AutoCloseable {
 		getRefDatabase().close();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public String toString() {
@@ -959,7 +1000,7 @@ public abstract class Repository implements AutoCloseable {
 	 *         an ObjectId in hex format if the current branch is detached, or
 	 *         {@code null} if the repository is corrupt and has no HEAD
 	 *         reference.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	@Nullable
 	public String getFullBranch() throws IOException {
@@ -987,7 +1028,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @return name of current branch (for example {@code master}), an ObjectId
 	 *         in hex format if the current branch is detached, or {@code null}
 	 *         if the repository is corrupt and has no HEAD reference.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	@Nullable
 	public String getBranch() throws IOException {
@@ -1020,7 +1061,7 @@ public abstract class Repository implements AutoCloseable {
 	 *            "master" which is is automatically expanded to
 	 *            "refs/heads/master" if "refs/heads/master" already exists.
 	 * @return the Ref with the given name, or {@code null} if it does not exist
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @deprecated Use {@link #exactRef(String)} or {@link #findRef(String)}
 	 * instead.
 	 */
@@ -1038,7 +1079,7 @@ public abstract class Repository implements AutoCloseable {
 	 *            form; e.g., "master" is not automatically expanded to
 	 *            "refs/heads/master".
 	 * @return the Ref with the given name, or {@code null} if it does not exist
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	@Nullable
@@ -1054,7 +1095,7 @@ public abstract class Repository implements AutoCloseable {
 	 *            "master" which is is automatically expanded to
 	 *            "refs/heads/master" if "refs/heads/master" already exists.
 	 * @return the Ref with the given name, or {@code null} if it does not exist
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	@Nullable
@@ -1063,6 +1104,8 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get mutable map of all known refs
+	 *
 	 * @return mutable map of all known refs (heads, tags, remotes).
 	 */
 	@NonNull
@@ -1075,6 +1118,8 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get mutable map of all tags
+	 *
 	 * @return mutable map of all tags; key is short tag name ("v1.0") and value
 	 *         of the entry contains the ref with the full tag name
 	 *         ("refs/tags/v1.0").
@@ -1092,7 +1137,8 @@ public abstract class Repository implements AutoCloseable {
 	 * Peel a possibly unpeeled reference to an annotated tag.
 	 * <p>
 	 * If the ref cannot be peeled (as it does not refer to an annotated tag)
-	 * the peeled id stays null, but {@link Ref#isPeeled()} will be true.
+	 * the peeled id stays null, but {@link org.eclipse.jgit.lib.Ref#isPeeled()}
+	 * will be true.
 	 *
 	 * @param ref
 	 *            The ref to peel
@@ -1114,6 +1160,8 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get a map with all objects referenced by a peeled ref.
+	 *
 	 * @return a map with all objects referenced by a peeled ref.
 	 */
 	@NonNull
@@ -1141,9 +1189,11 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get the index file location or {@code null} if repository isn't local.
+	 *
 	 * @return the index file location or {@code null} if repository isn't
 	 *         local.
-	 * @throws NoWorkTreeException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1163,11 +1213,11 @@ public abstract class Repository implements AutoCloseable {
 	 * @param id
 	 *            name of the commit object.
 	 * @return reference to the commit object. Never null.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the supplied commit does not exist.
-	 * @throws IncorrectObjectTypeException
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             the supplied id is not a commit or an annotated tag.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
 	 * @since 4.8
 	 */
@@ -1190,12 +1240,12 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
-	 * @throws NoWorkTreeException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the index file is present but could not be read.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
@@ -1214,13 +1264,13 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
-	 * @throws NoWorkTreeException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the index file is present but could not be read, or the lock
 	 *             could not be obtained.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
@@ -1239,7 +1289,9 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
-	 * @return an important state
+	 * Get the repository state
+	 *
+	 * @return the repository state
 	 */
 	@NonNull
 	public RepositoryState getRepositoryState() {
@@ -1320,8 +1372,7 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * For portability reasons '\' is excluded
 	 *
-	 * @param refName
-	 *
+	 * @param refName a {@link java.lang.String} object.
 	 * @return true if refName is a valid ref name
 	 */
 	public static boolean isValidRefName(final String refName) {
@@ -1392,7 +1443,6 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @param name
 	 *            to normalize
-	 *
 	 * @return The normalized name or an empty String if it is {@code null} or
 	 *         empty.
 	 * @since 4.7
@@ -1499,6 +1549,8 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Whether this repository is bare
+	 *
 	 * @return true if this is bare, which implies it has no working directory.
 	 */
 	public boolean isBare() {
@@ -1506,9 +1558,12 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get the root directory of the working tree, where files are checked out
+	 * for viewing and editing.
+	 *
 	 * @return the root directory of the working tree, where files are checked
 	 *         out for viewing and editing.
-	 * @throws NoWorkTreeException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1522,7 +1577,7 @@ public abstract class Repository implements AutoCloseable {
 	/**
 	 * Force a scan for changed refs.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public abstract void scanForRepoChanges() throws IOException;
 
@@ -1532,8 +1587,10 @@ public abstract class Repository implements AutoCloseable {
 	public abstract void notifyIndexChanged();
 
 	/**
-	 * @param refName
+	 * Get a shortened more user friendly ref name
 	 *
+	 * @param refName
+	 *            a {@link java.lang.String} object.
 	 * @return a more user friendly ref name
 	 */
 	@NonNull
@@ -1548,7 +1605,10 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get a shortened more user friendly remote tracking branch name
+	 *
 	 * @param refName
+	 *            a {@link java.lang.String} object.
 	 * @return the remote branch name part of <code>refName</code>, i.e. without
 	 *         the <code>refs/remotes/&lt;remote&gt;</code> prefix, if
 	 *         <code>refName</code> represents a remote tracking branch;
@@ -1566,7 +1626,10 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get remote name
+	 *
 	 * @param refName
+	 *            a {@link java.lang.String} object.
 	 * @return the remote name part of <code>refName</code>, i.e. without the
 	 *         <code>refs/remotes/&lt;remote&gt;</code> prefix, if
 	 *         <code>refName</code> represents a remote tracking branch;
@@ -1587,7 +1650,7 @@ public abstract class Repository implements AutoCloseable {
 	 * Read the {@code GIT_DIR/description} file for gitweb.
 	 *
 	 * @return description text; null if no description has been configured.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             description cannot be accessed.
 	 * @since 4.6
 	 */
@@ -1601,7 +1664,7 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @param description
 	 *            new description; null to clear the description.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             description cannot be persisted.
 	 * @since 4.6
 	 */
@@ -1611,10 +1674,13 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get the reflog reader
+	 *
 	 * @param refName
-	 * @return a {@link ReflogReader} for the supplied refname, or {@code null}
-	 *         if the named ref does not exist.
-	 * @throws IOException
+	 *            a {@link java.lang.String} object.
+	 * @return a {@link org.eclipse.jgit.lib.ReflogReader} for the supplied
+	 *         refname, or {@code null} if the named ref does not exist.
+	 * @throws java.io.IOException
 	 *             the ref could not be accessed.
 	 * @since 3.0
 	 */
@@ -1629,8 +1695,8 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @return a String containing the content of the MERGE_MSG file or
 	 *         {@code null} if this file doesn't exist
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1648,8 +1714,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param msg
 	 *            the message which should be written or <code>null</code> to
 	 *            delete the file
-	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeMergeCommitMsg(String msg) throws IOException {
 		File mergeMsgFile = new File(gitDir, Constants.MERGE_MSG);
@@ -1663,8 +1728,8 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @return a String containing the content of the COMMIT_EDITMSG file or
 	 *         {@code null} if this file doesn't exist
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 * @since 4.0
@@ -1682,8 +1747,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param msg
 	 *            the message which should be written or {@code null} to delete
 	 *            the file
-	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.0
 	 */
 	public void writeCommitEditMsg(String msg) throws IOException {
@@ -1699,8 +1763,8 @@ public abstract class Repository implements AutoCloseable {
 	 * @return a list of commits which IDs are listed in the MERGE_HEAD file or
 	 *         {@code null} if this file doesn't exist. Also if the file exists
 	 *         but is empty {@code null} will be returned
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1731,7 +1795,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param heads
 	 *            a list of commits which IDs should be written to
 	 *            $GIT_DIR/MERGE_HEAD or <code>null</code> to delete the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeMergeHeads(List<? extends ObjectId> heads) throws IOException {
 		writeHeadsFile(heads, Constants.MERGE_HEAD);
@@ -1743,8 +1807,8 @@ public abstract class Repository implements AutoCloseable {
 	 * @return object id from CHERRY_PICK_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1767,8 +1831,8 @@ public abstract class Repository implements AutoCloseable {
 	 * @return object id from REVERT_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1790,7 +1854,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param head
 	 *            an object id of the cherry commit or <code>null</code> to
 	 *            delete the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeCherryPickHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = (head != null) ? Collections.singletonList(head)
@@ -1805,7 +1869,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param head
 	 *            an object id of the revert commit or <code>null</code> to
 	 *            delete the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeRevertHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = (head != null) ? Collections.singletonList(head)
@@ -1819,7 +1883,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param head
 	 *            an object id of the original HEAD commit or <code>null</code>
 	 *            to delete the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeOrigHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = head != null ? Collections.singletonList(head)
@@ -1833,8 +1897,8 @@ public abstract class Repository implements AutoCloseable {
 	 * @return object id from ORIG_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
-	 * @throws IOException
-	 * @throws NoWorkTreeException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.errors.NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
@@ -1854,7 +1918,7 @@ public abstract class Repository implements AutoCloseable {
 	 *
 	 * @return a String containing the content of the SQUASH_MSG file or
 	 *         {@code null} if this file doesn't exist
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
@@ -1873,8 +1937,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param msg
 	 *            the message which should be written or <code>null</code> to
 	 *            delete the file
-	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void writeSquashCommitMsg(String msg) throws IOException {
 		File squashMsgFile = new File(gitDir, Constants.SQUASH_MSG);
@@ -1970,7 +2033,7 @@ public abstract class Repository implements AutoCloseable {
 	 * @param includeComments
 	 *            <code>true</code> if also comments should be reported
 	 * @return the list of steps
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.2
 	 */
 	@NonNull
@@ -1990,7 +2053,7 @@ public abstract class Repository implements AutoCloseable {
 	 *            the steps to be written
 	 * @param append
 	 *            whether to append to an existing file or to write a new file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.2
 	 */
 	public void writeRebaseTodoFile(String path, List<RebaseTodoLine> steps,
@@ -2000,6 +2063,8 @@ public abstract class Repository implements AutoCloseable {
 	}
 
 	/**
+	 * Get the names of all known remotes
+	 *
 	 * @return the names of all known remotes
 	 * @since 3.4
 	 */
@@ -2016,7 +2081,8 @@ public abstract class Repository implements AutoCloseable {
 	 * objects.
 	 * <p/>
 	 * Currently this option is supported for repositories of type
-	 * {@code FileRepository} only. See {@link GC#setAuto(boolean)} for
+	 * {@code FileRepository} only. See
+	 * {@link org.eclipse.jgit.internal.storage.file.GC#setAuto(boolean)} for
 	 * configuration details.
 	 *
 	 * @param monitor

org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryBuilder.java

@@ -46,7 +46,7 @@ package org.eclipse.jgit.lib;
 import java.io.File;
 
 /**
- * Base class to support constructing a {@link Repository}.
+ * Base class to support constructing a {@link org.eclipse.jgit.lib.Repository}.
  * <p>
  * Applications must set one of {@link #setGitDir(File)} or
  * {@link #setWorkTree(File)}, or use {@link #readEnvironment()} or

org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java

@@ -62,7 +62,9 @@ import org.eclipse.jgit.util.RawParseUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-/** Cache of active {@link Repository} instances. */
+/**
+ * Cache of active {@link org.eclipse.jgit.lib.Repository} instances.
+ */
 public class RepositoryCache {
 	private final static Logger LOG = LoggerFactory
 			.getLogger(RepositoryCache.class);
@@ -73,15 +75,17 @@ public class RepositoryCache {
 	 * Open an existing repository, reusing a cached instance if possible.
 	 * <p>
 	 * When done with the repository, the caller must call
-	 * {@link Repository#close()} to decrement the repository's usage counter.
+	 * {@link org.eclipse.jgit.lib.Repository#close()} to decrement the
+	 * repository's usage counter.
 	 *
 	 * @param location
-	 *            where the local repository is. Typically a {@link FileKey}.
+	 *            where the local repository is. Typically a
+	 *            {@link org.eclipse.jgit.lib.RepositoryCache.FileKey}.
 	 * @return the repository instance requested; caller must close when done.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be read (likely its core.version
 	 *             property is not supported).
-	 * @throws RepositoryNotFoundException
+	 * @throws org.eclipse.jgit.errors.RepositoryNotFoundException
 	 *             there is no repository at the given location.
 	 */
 	public static Repository open(final Key location) throws IOException,
@@ -93,16 +97,18 @@ public class RepositoryCache {
 	 * Open a repository, reusing a cached instance if possible.
 	 * <p>
 	 * When done with the repository, the caller must call
-	 * {@link Repository#close()} to decrement the repository's usage counter.
+	 * {@link org.eclipse.jgit.lib.Repository#close()} to decrement the
+	 * repository's usage counter.
 	 *
 	 * @param location
-	 *            where the local repository is. Typically a {@link FileKey}.
+	 *            where the local repository is. Typically a
+	 *            {@link org.eclipse.jgit.lib.RepositoryCache.FileKey}.
 	 * @param mustExist
 	 *            If true, and the repository is not found, throws {@code
 	 *            RepositoryNotFoundException}. If false, a repository instance
 	 *            is created and registered anyway.
 	 * @return the repository instance requested; caller must close when done.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be read (likely its core.version
 	 *             property is not supported).
 	 * @throws RepositoryNotFoundException
@@ -118,9 +124,10 @@ public class RepositoryCache {
 	 * Register one repository into the cache.
 	 * <p>
 	 * During registration the cache automatically increments the usage counter,
-	 * permitting it to retain the reference. A {@link FileKey} for the
-	 * repository's {@link Repository#getDirectory()} is used to index the
-	 * repository in the cache.
+	 * permitting it to retain the reference. A
+	 * {@link org.eclipse.jgit.lib.RepositoryCache.FileKey} for the repository's
+	 * {@link org.eclipse.jgit.lib.Repository#getDirectory()} is used to index
+	 * the repository in the cache.
 	 * <p>
 	 * If another repository already is registered in the cache at this
 	 * location, the other instance is closed.
@@ -156,8 +163,8 @@ public class RepositoryCache {
 	 * <p>
 	 * Removes a repository from the cache, if it is still registered here. This
 	 * method will not close the repository, only remove it from the cache. See
-	 * {@link RepositoryCache#close(Repository)} to remove and close the
-	 * repository.
+	 * {@link org.eclipse.jgit.lib.RepositoryCache#close(Repository)} to remove
+	 * and close the repository.
 	 *
 	 * @param db
 	 *            repository to unregister.
@@ -174,8 +181,8 @@ public class RepositoryCache {
 	 * <p>
 	 * Removes a repository from the cache, if it is still registered here. This
 	 * method will not close the repository, only remove it from the cache. See
-	 * {@link RepositoryCache#close(Repository)} to remove and close the
-	 * repository.
+	 * {@link org.eclipse.jgit.lib.RepositoryCache#close(Repository)} to remove
+	 * and close the repository.
 	 *
 	 * @param location
 	 *            location of the repository to remove.
@@ -186,6 +193,8 @@ public class RepositoryCache {
 	}
 
 	/**
+	 * Get the locations of all repositories registered in the cache.
+	 *
 	 * @return the locations of all repositories registered in the cache.
 	 * @since 4.1
 	 */
@@ -202,7 +211,9 @@ public class RepositoryCache {
 		return cache.cacheMap.get(key) == repo;
 	}
 
-	/** Unregister all repositories from the cache. */
+	/**
+	 * Unregister all repositories from the cache.
+	 */
 	public static void clear() {
 		cache.clearAll();
 	}

org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCacheConfig.java

@@ -68,23 +68,32 @@ public class RepositoryCacheConfig {
 
 	private long cleanupDelayMillis;
 
-	/** Create a default configuration. */
+	/**
+	 * Create a default configuration.
+	 */
 	public RepositoryCacheConfig() {
 		expireAfterMillis = TimeUnit.HOURS.toMillis(1);
 		cleanupDelayMillis = AUTO_CLEANUP_DELAY;
 	}
 
 	/**
-	 * @return the time an unused repository should expired and be evicted from
-	 *         the RepositoryCache in milliseconds. <b>Default is 1 hour.</b>
+	 * Get the time an unused repository should be expired and be evicted from
+	 * the RepositoryCache in milliseconds.
+	 *
+	 * @return the time an unused repository should be expired and be evicted
+	 *         from the RepositoryCache in milliseconds. <b>Default is 1
+	 *         hour.</b>
 	 */
 	public long getExpireAfter() {
 		return expireAfterMillis;
 	}
 
 	/**
+	 * Set the time an unused repository should be expired and be evicted from
+	 * the RepositoryCache in milliseconds.
+	 *
 	 * @param expireAfterMillis
-	 *            the time an unused repository should expired and be evicted
+	 *            the time an unused repository should be expired and be evicted
 	 *            from the RepositoryCache in milliseconds.
 	 */
 	public void setExpireAfter(long expireAfterMillis) {
@@ -92,6 +101,9 @@ public class RepositoryCacheConfig {
 	}
 
 	/**
+	 * Get the delay between the periodic cleanup of expired repository in
+	 * milliseconds.
+	 *
 	 * @return the delay between the periodic cleanup of expired repository in
 	 *         milliseconds. <b>Default is minimum of 1/10 of expireAfterMillis
 	 *         and 10 minutes</b>
@@ -105,6 +117,9 @@ public class RepositoryCacheConfig {
 	}
 
 	/**
+	 * Set the delay between the periodic cleanup of expired repository in
+	 * milliseconds.
+	 *
 	 * @param cleanupDelayMillis
 	 *            the delay between the periodic cleanup of expired repository
 	 *            in milliseconds. Set it to {@link #AUTO_CLEANUP_DELAY} to

org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryState.java

@@ -381,7 +381,9 @@ public enum RepositoryState {
 	};
 
 	/**
-	 * @return true if changing HEAD is sane.
+	 * Whether checkout can be done.
+	 *
+	 * @return whether checkout can be done.
 	 */
 	public abstract boolean canCheckout();
 

org.eclipse.jgit/src/org/eclipse/jgit/lib/StoredConfig.java

@@ -51,7 +51,9 @@ import org.eclipse.jgit.errors.ConfigInvalidException;
  * Persistent configuration that can be stored and loaded from a location.
  */
 public abstract class StoredConfig extends Config {
-	/** Create a configuration with no default fallback. */
+	/**
+	 * Create a configuration with no default fallback.
+	 */
 	public StoredConfig() {
 		super();
 	}
@@ -73,9 +75,9 @@ public abstract class StoredConfig extends Config {
 	 * If the configuration does not exist, this configuration is cleared, and
 	 * thus behaves the same as though the backing store exists, but is empty.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the configuration could not be read (but does exist).
-	 * @throws ConfigInvalidException
+	 * @throws org.eclipse.jgit.errors.ConfigInvalidException
 	 *             the configuration is not properly formatted.
 	 */
 	public abstract void load() throws IOException, ConfigInvalidException;
@@ -83,11 +85,12 @@ public abstract class StoredConfig extends Config {
 	/**
 	 * Save the configuration to the persistent store.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the configuration could not be written.
 	 */
 	public abstract void save() throws IOException;
 
+	/** {@inheritDoc} */
 	@Override
 	public void clear() {
 		super.clear();

org.eclipse.jgit/src/org/eclipse/jgit/lib/SymbolicRef.java

@@ -47,7 +47,8 @@ import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 
 /**
- * A reference that indirectly points at another {@link Ref}.
+ * A reference that indirectly points at another
+ * {@link org.eclipse.jgit.lib.Ref}.
  * <p>
  * A symbolic reference always derives its current value from the target
  * reference.
@@ -70,17 +71,20 @@ public class SymbolicRef implements Ref {
 		this.target = target;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public String getName() {
 		return name;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isSymbolic() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Ref getLeaf() {
@@ -90,35 +94,41 @@ public class SymbolicRef implements Ref {
 		return dst;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Ref getTarget() {
 		return target;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@Nullable
 	public ObjectId getObjectId() {
 		return getLeaf().getObjectId();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@NonNull
 	public Storage getStorage() {
 		return Storage.LOOSE;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@Nullable
 	public ObjectId getPeeledObjectId() {
 		return getLeaf().getPeeledObjectId();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isPeeled() {
 		return getLeaf().isPeeled();
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/TagBuilder.java

@@ -72,12 +72,20 @@ public class TagBuilder {
 
 	private String message;
 
-	/** @return the type of object this tag refers to. */
+	/**
+	 * Get the type of object this tag refers to.
+	 *
+	 * @return the type of object this tag refers to.
+	 */
 	public int getObjectType() {
 		return type;
 	}
 
-	/** @return the object this tag refers to. */
+	/**
+	 * Get the object this tag refers to.
+	 *
+	 * @return the object this tag refers to.
+	 */
 	public ObjectId getObjectId() {
 		return object;
 	}
@@ -105,7 +113,11 @@ public class TagBuilder {
 		setObjectId(obj, obj.getType());
 	}
 
-	/** @return short name of the tag (no {@code refs/tags/} prefix). */
+	/**
+	 * Get short name of the tag (no {@code refs/tags/} prefix).
+	 *
+	 * @return short name of the tag (no {@code refs/tags/} prefix).
+	 */
 	public String getTag() {
 		return tag;
 	}
@@ -122,7 +134,11 @@ public class TagBuilder {
 		this.tag = shortName;
 	}
 
-	/** @return creator of this tag. May be null. */
+	/**
+	 * Get creator of this tag.
+	 *
+	 * @return creator of this tag. May be null.
+	 */
 	public PersonIdent getTagger() {
 		return tagger;
 	}
@@ -137,7 +153,11 @@ public class TagBuilder {
 		tagger = taggerIdent;
 	}
 
-	/** @return the complete commit message. */
+	/**
+	 * Get the complete commit message.
+	 *
+	 * @return the complete commit message.
+	 */
 	public String getMessage() {
 		return message;
 	}
@@ -203,6 +223,7 @@ public class TagBuilder {
 		return build();
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/TextProgressMonitor.java

@@ -51,13 +51,17 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.io.Writer;
 
-/** A simple progress reporter printing on a stream. */
+/**
+ * A simple progress reporter printing on a stream.
+ */
 public class TextProgressMonitor extends BatchingProgressMonitor {
 	private final Writer out;
 
 	private boolean write;
 
-	/** Initialize a new progress monitor. */
+	/**
+	 * Initialize a new progress monitor.
+	 */
 	public TextProgressMonitor() {
 		this(new PrintWriter(new OutputStreamWriter(System.err, UTF_8)));
 	}
@@ -73,6 +77,7 @@ public class TextProgressMonitor extends BatchingProgressMonitor {
 		this.write = true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onUpdate(String taskName, int workCurr) {
 		StringBuilder s = new StringBuilder();
@@ -80,6 +85,7 @@ public class TextProgressMonitor extends BatchingProgressMonitor {
 		send(s);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndTask(String taskName, int workCurr) {
 		StringBuilder s = new StringBuilder();
@@ -97,6 +103,7 @@ public class TextProgressMonitor extends BatchingProgressMonitor {
 		s.append(workCurr);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onUpdate(String taskName, int cmp, int totalWork, int pcnt) {
 		StringBuilder s = new StringBuilder();
@@ -104,6 +111,7 @@ public class TextProgressMonitor extends BatchingProgressMonitor {
 		send(s);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndTask(String taskName, int cmp, int totalWork, int pcnt) {
 		StringBuilder s = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/lib/ThreadSafeProgressMonitor.java

@@ -48,7 +48,8 @@ import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.locks.ReentrantLock;
 
 /**
- * Wrapper around the general {@link ProgressMonitor} to make it thread safe.
+ * Wrapper around the general {@link org.eclipse.jgit.lib.ProgressMonitor} to
+ * make it thread safe.
  *
  * Updates to the underlying ProgressMonitor are made only from the thread that
  * allocated this wrapper. Callers are responsible for ensuring the allocating
@@ -87,6 +88,7 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 		this.process = new Semaphore(0);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void start(int totalTasks) {
 		if (!isMainThread())
@@ -94,6 +96,7 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 		pm.start(totalTasks);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void beginTask(String title, int totalWork) {
 		if (!isMainThread())
@@ -101,7 +104,9 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 		pm.beginTask(title, totalWork);
 	}
 
-	/** Notify the monitor a worker is starting. */
+	/**
+	 * Notify the monitor a worker is starting.
+	 */
 	public void startWorker() {
 		startWorkers(1);
 	}
@@ -116,7 +121,9 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 		workers.addAndGet(count);
 	}
 
-	/** Notify the monitor a worker is finished. */
+	/**
+	 * Notify the monitor a worker is finished.
+	 */
 	public void endWorker() {
 		if (workers.decrementAndGet() == 0)
 			process.release();
@@ -139,7 +146,7 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 	 * This method can only be invoked by the same thread that allocated this
 	 * ThreadSafeProgressMonior.
 	 *
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             if the main thread is interrupted while waiting for
 	 *             completion of workers.
 	 */
@@ -158,12 +165,14 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 			pm.update(cnt);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void update(int completed) {
 		if (0 == pendingUpdates.getAndAdd(completed))
 			process.release();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isCancelled() {
 		lock.lock();
@@ -174,6 +183,7 @@ public class ThreadSafeProgressMonitor implements ProgressMonitor {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void endTask() {
 		if (!isMainThread())

org.eclipse.jgit/src/org/eclipse/jgit/lib/TreeFormatter.java

@@ -94,7 +94,9 @@ public class TreeFormatter {
 
 	private TemporaryBuffer.Heap overflowBuffer;
 
-	/** Create an empty formatter with a default buffer size. */
+	/**
+	 * Create an empty formatter with a default buffer size.
+	 */
 	public TreeFormatter() {
 		this(8192);
 	}
@@ -112,7 +114,7 @@ public class TreeFormatter {
 	}
 
 	/**
-	 * Add a link to a submodule commit, mode is {@link FileMode#GITLINK}.
+	 * Add a link to a submodule commit, mode is {@link org.eclipse.jgit.lib.FileMode#GITLINK}.
 	 *
 	 * @param name
 	 *            name of the entry.
@@ -124,7 +126,7 @@ public class TreeFormatter {
 	}
 
 	/**
-	 * Add a subtree, mode is {@link FileMode#TREE}.
+	 * Add a subtree, mode is {@link org.eclipse.jgit.lib.FileMode#TREE}.
 	 *
 	 * @param name
 	 *            name of the entry.
@@ -136,7 +138,7 @@ public class TreeFormatter {
 	}
 
 	/**
-	 * Add a regular file, mode is {@link FileMode#REGULAR_FILE}.
+	 * Add a regular file, mode is {@link org.eclipse.jgit.lib.FileMode#REGULAR_FILE}.
 	 *
 	 * @param name
 	 *            name of the entry.
@@ -307,7 +309,7 @@ public class TreeFormatter {
 	 * @param ins
 	 *            the inserter to store the tree.
 	 * @return computed ObjectId of the tree
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the tree could not be stored.
 	 */
 	public ObjectId insertTo(ObjectInserter ins) throws IOException {
@@ -321,7 +323,7 @@ public class TreeFormatter {
 	/**
 	 * Compute the ObjectId for this tree
 	 *
-	 * @param ins
+	 * @param ins a {@link org.eclipse.jgit.lib.ObjectInserter} object.
 	 * @return ObjectId for this tree
 	 */
 	public ObjectId computeId(ObjectInserter ins) {
@@ -343,7 +345,8 @@ public class TreeFormatter {
 	 * This method is not efficient, as it needs to create a copy of the
 	 * internal buffer in order to supply an array of the correct size to the
 	 * caller. If the buffer is just to pass to an ObjectInserter, consider
-	 * using {@link ObjectInserter#insert(TreeFormatter)} instead.
+	 * using {@link org.eclipse.jgit.lib.ObjectInserter#insert(TreeFormatter)}
+	 * instead.
 	 *
 	 * @return a copy of this formatter's buffer.
 	 */
@@ -362,6 +365,7 @@ public class TreeFormatter {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/lib/TypedConfigGetter.java

@@ -50,15 +50,15 @@ import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.transport.RefSpec;
 
 /**
- * Something that knows how to convert plain strings from a git {@link Config}
- * to typed values.
+ * Something that knows how to convert plain strings from a git
+ * {@link org.eclipse.jgit.lib.Config} to typed values.
  *
  * @since 4.9
  */
 public interface TypedConfigGetter {
 
 	/**
-	 * Get a boolean value from a git {@link Config}.
+	 * Get a boolean value from a git {@link org.eclipse.jgit.lib.Config}.
 	 *
 	 * @param config
 	 *            to get the value from
@@ -77,10 +77,8 @@ public interface TypedConfigGetter {
 			String name, boolean defaultValue);
 
 	/**
-	 * Parse an enumeration from a git {@link Config}.
+	 * Parse an enumeration from a git {@link org.eclipse.jgit.lib.Config}.
 	 *
-	 * @param <T>
-	 *            type of the enumeration object.
 	 * @param config
 	 *            to get the value from
 	 * @param all
@@ -100,7 +98,7 @@ public interface TypedConfigGetter {
 			String subsection, String name, T defaultValue);
 
 	/**
-	 * Obtain an integer value from a git {@link Config}.
+	 * Obtain an integer value from a git {@link org.eclipse.jgit.lib.Config}.
 	 *
 	 * @param config
 	 *            to get the value from
@@ -118,7 +116,7 @@ public interface TypedConfigGetter {
 			int defaultValue);
 
 	/**
-	 * Obtain a long value from a git {@link Config}.
+	 * Obtain a long value from a git {@link org.eclipse.jgit.lib.Config}.
 	 *
 	 * @param config
 	 *            to get the value from
@@ -137,7 +135,7 @@ public interface TypedConfigGetter {
 
 	/**
 	 * Parse a numerical time unit, such as "1 minute", from a git
-	 * {@link Config}.
+	 * {@link org.eclipse.jgit.lib.Config}.
 	 *
 	 * @param config
 	 *            to get the value from
@@ -161,7 +159,8 @@ public interface TypedConfigGetter {
 
 
 	/**
-	 * Parse a list of {@link RefSpec}s from a git {@link Config}.
+	 * Parse a list of {@link org.eclipse.jgit.transport.RefSpec}s from a git
+	 * {@link org.eclipse.jgit.lib.Config}.
 	 *
 	 * @param config
 	 *            to get the list from
@@ -171,7 +170,8 @@ public interface TypedConfigGetter {
 	 *            subsection the key is in, or null if not in a subsection.
 	 * @param name
 	 *            the key name.
-	 * @return a possibly empty list of {@link RefSpec}s
+	 * @return a possibly empty list of
+	 *         {@link org.eclipse.jgit.transport.RefSpec}s
 	 */
 	@NonNull
 	List<RefSpec> getRefSpecs(Config config, String section, String subsection,

org.eclipse.jgit/src/org/eclipse/jgit/lib/UserConfig.java

@@ -48,7 +48,9 @@ package org.eclipse.jgit.lib;
 import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.util.SystemReader;
 
-/** The standard "user" configuration parameters. */
+/**
+ * The standard "user" configuration parameters.
+ */
 public class UserConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
 	public static final Config.SectionParser<UserConfig> KEY = UserConfig::new;
@@ -94,6 +96,8 @@ public class UserConfig {
 	}
 
 	/**
+	 * Get the author name as defined in the git variables and configurations.
+	 *
 	 * @return the author name as defined in the git variables and
 	 *         configurations. If no name could be found, try to use the system
 	 *         user name instead.
@@ -103,6 +107,9 @@ public class UserConfig {
 	}
 
 	/**
+	 * Get the committer name as defined in the git variables and
+	 * configurations.
+	 *
 	 * @return the committer name as defined in the git variables and
 	 *         configurations. If no name could be found, try to use the system
 	 *         user name instead.
@@ -112,26 +119,31 @@ public class UserConfig {
 	}
 
 	/**
-	 * @return the author email as defined in git variables and
-	 *         configurations. If no email could be found, try to
-	 *         propose one default with the user name and the
-	 *         host name.
+	 * Get the author email as defined in git variables and configurations.
+	 *
+	 * @return the author email as defined in git variables and configurations.
+	 *         If no email could be found, try to propose one default with the
+	 *         user name and the host name.
 	 */
 	public String getAuthorEmail() {
 		return authorEmail;
 	}
 
 	/**
+	 * Get the committer email as defined in git variables and configurations.
+	 *
 	 * @return the committer email as defined in git variables and
-	 *         configurations. If no email could be found, try to
-	 *         propose one default with the user name and the
-	 *         host name.
+	 *         configurations. If no email could be found, try to propose one
+	 *         default with the user name and the host name.
 	 */
 	public String getCommitterEmail() {
 		return committerEmail;
 	}
 
 	/**
+	 * Whether the author name was not explicitly configured but constructed
+	 * from information the system has about the logged on user
+	 *
 	 * @return true if the author name was not explicitly configured but
 	 *         constructed from information the system has about the logged on
 	 *         user
@@ -141,6 +153,9 @@ public class UserConfig {
 	}
 
 	/**
+	 * Whether the author email was not explicitly configured but constructed
+	 * from information the system has about the logged on user
+	 *
 	 * @return true if the author email was not explicitly configured but
 	 *         constructed from information the system has about the logged on
 	 *         user
@@ -150,6 +165,9 @@ public class UserConfig {
 	}
 
 	/**
+	 * Whether the committer name was not explicitly configured but constructed
+	 * from information the system has about the logged on user
+	 *
 	 * @return true if the committer name was not explicitly configured but
 	 *         constructed from information the system has about the logged on
 	 *         user
@@ -159,6 +177,9 @@ public class UserConfig {
 	}
 
 	/**
+	 * Whether the author email was not explicitly configured but constructed
+	 * from information the system has about the logged on user
+	 *
 	 * @return true if the author email was not explicitly configured but
 	 *         constructed from information the system has about the logged on
 	 *         user

org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/WorkQueue.java

@@ -95,6 +95,8 @@ public class WorkQueue {
 	}
 
 	/**
+	 * Get the WorkQueue's executor
+	 *
 	 * @return the WorkQueue's executor
 	 */
 	public static ScheduledThreadPoolExecutor getExecutor() {