Fix trivial usages of deprecated Repository#getAllRefs

Callers of getAllRefs that only iterate over the `values()` of the
returned map can be trivially fixed to call getRefDatabase().getRefs()
instead.

Only fix those where the calling method is already declared to throw
IOException, to avoid potential API changes.

Change-Id: I2b05f785077a1713953cfd42df7bf915f889f90b
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java

@@ -757,7 +757,7 @@ public class TestRepository<R extends Repository> {
 	public void updateServerInfo() throws Exception {
 		if (db instanceof FileRepository) {
 			final FileRepository fr = (FileRepository) db;
-			RefWriter rw = new RefWriter(fr.getAllRefs().values()) {
+			RefWriter rw = new RefWriter(fr.getRefDatabase().getRefs()) {
 				@Override
 				protected void writeFile(String name, byte[] bin)
 						throws IOException {
@@ -852,7 +852,7 @@ public class TestRepository<R extends Repository> {
 				for (RevObject o : tips)
 					ow.markStart(ow.parseAny(o));
 			} else {
-				for (Ref r : db.getAllRefs().values())
+				for (Ref r : db.getRefDatabase().getRefs())
 					ow.markStart(ow.parseAny(r.getObjectId()));
 			}
 
@@ -905,7 +905,7 @@ public class TestRepository<R extends Repository> {
 			final File pack, idx;
 			try (PackWriter pw = new PackWriter(db)) {
 				Set<ObjectId> all = new HashSet<>();
-				for (Ref r : db.getAllRefs().values())
+				for (Ref r : db.getRefDatabase().getRefs())
 					all.add(r.getObjectId());
 				pw.preparePack(m, all, PackWriter.NONE);
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java

@@ -245,7 +245,7 @@ public class PushCommandTest extends RepositoryTestCase {
 				git.add().addFilepattern("f" + i).call();
 				commit = git.commit().setMessage("adding f" + i).call();
 				git.push().setRemote("test").call();
-				git2.getRepository().getAllRefs();
+				git2.getRepository().getRefDatabase().getRefs();
 				assertEquals("failed to update on attempt " + i, commit.getId(),
 						git2.getRepository().resolve("refs/heads/test"));
 			}

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java

@@ -972,7 +972,7 @@ public class DfsGarbageCollectorTest {
 	private static boolean isReachable(Repository repo, AnyObjectId id)
 			throws IOException {
 		try (RevWalk rw = new RevWalk(repo)) {
-			for (Ref ref : repo.getAllRefs().values()) {
+			for (Ref ref : repo.getRefDatabase().getRefs()) {
 				rw.markStart(rw.parseCommit(ref.getObjectId()));
 			}
 			for (RevCommit next; (next = rw.next()) != null;) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkUtilsReachableTest.java

@@ -115,7 +115,7 @@ public class RevWalkUtilsReachableTest extends RevWalkTestCase {
 	}
 
 	private void assertContains(RevCommit commit, Collection<Ref> refsThatShouldContainCommit) throws Exception {
-		Collection<Ref> allRefs = db.getAllRefs().values();
+		Collection<Ref> allRefs = db.getRefDatabase().getRefs();
 		Collection<Ref> sortedRefs = RefComparator.sort(allRefs);
 		List<Ref> actual = RevWalkUtils.findBranchesReachableFrom(commit,
 				rw, sortedRefs);

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java

@@ -146,7 +146,7 @@ public class DfsFsck {
 			throws IOException {
 		pm.beginTask(JGitText.get().countingObjects, ProgressMonitor.UNKNOWN);
 		try (ObjectWalk ow = new ObjectWalk(repo)) {
-			for (Ref r : repo.getAllRefs().values()) {
+			for (Ref r : repo.getRefDatabase().getRefs()) {
 				ObjectId objectId = r.getObjectId();
 				if (objectId == null) {
 					// skip unborn branch