Repository: Deprecate the #getAllRefs method

Callers should instead use getRefDatabase().getRefs(), which does not
swallow the IOException.

Replace @link with @code in the Javadoc of FileRepository, since linking
to the deprecated method causes an error:

  Javadoc: The method getAllRefs() from the type Repository is deprecated

Existing callers of the deprecated method are not adapted in this commit
because many of them require more refactoring. They will be done in
separate follow-up commits.

Bug: 534731
Change-Id: Id84e70e4cd7be3d1ca1795512950c6abe3d18ffd
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java

@@ -477,7 +477,7 @@ public class FileRepository extends Repository {
 	/**
 	 * {@inheritDoc}
 	 * <p>
-	 * Objects known to exist but not expressed by {@link #getAllRefs()}.
+	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
 	 * <p>
 	 * When a repository borrows objects from another repository, it can
 	 * advertise that it safely has that other repository's references, without
@@ -490,12 +490,12 @@ public class FileRepository extends Repository {
 	}
 
 	/**
-	 * Objects known to exist but not expressed by {@link #getAllRefs()}.
+	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
 	 * <p>
 	 * When a repository borrows objects from another repository, it can
 	 * advertise that it safely has that other repository's references, without
-	 * exposing any other details about the other repository.  This may help
-	 * a client trying to push changes avoid pushing more than it needs to.
+	 * exposing any other details about the other repository. This may help a
+	 * client trying to push changes avoid pushing more than it needs to.
 	 *
 	 * @param skips
 	 *            Set of AlternateHandle Ids already seen

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

@@ -1092,7 +1092,9 @@ public abstract class Repository implements AutoCloseable {
 	 * not point to any object yet.
 	 *
 	 * @return mutable map of all known refs (heads, tags, remotes).
+	 * @deprecated use {@code getRefDatabase().getRefs()} instead.
 	 */
+	@Deprecated
 	@NonNull
 	public Map<String, Ref> getAllRefs() {
 		try {