Add missing @Deprecated to deprecated fields and methods

Java spec requires the @Deprecated annotation on any deprecated
field or method. Add the missing annotation to fields and methods
already declared deprecated in the javadoc.

Change-Id: Ic0ef24b43cfd99ac947e771ef5a28e493c304274

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java

@@ -103,6 +103,7 @@ public abstract class TextBuiltin {
 	 *
 	 * @deprecated Use outw instead
 	 */
+	@Deprecated
 	protected PrintWriter out;
 
 	/** Git repository the command was invoked within. */

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java

@@ -810,6 +810,7 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	 * @return true if content is most likely different.
 	 * @deprecated Use {@link #isModified(DirCacheEntry, boolean, ObjectReader)}
 	 */
+	@Deprecated
 	public boolean isModified(DirCacheEntry entry, boolean forceContentCheck) {
 		try {
 			return isModified(entry, forceContentCheck, null);