Merge changes from topic 'includeDeletes'

* changes:
  Add flag for keeping ref tombstones in GC reftable
  Preserve ref tombstone when compact top retable stack

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

@@ -587,6 +587,7 @@ public class TestRepository<R extends Repository> {
 	public void delete(String ref) throws Exception {
 		ref = normalizeRef(ref);
 		RefUpdate u = db.updateRef(ref);
+		u.setForceUpdate(true);
 		switch (u.delete()) {
 		case FAST_FORWARD:
 		case FORCED:

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

@@ -9,6 +9,7 @@ import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -18,6 +19,7 @@ import java.util.Collections;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource;
+import org.eclipse.jgit.internal.storage.dfs.DfsRefDatabase;
 import org.eclipse.jgit.internal.storage.reftable.RefCursor;
 import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
 import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
@@ -842,6 +844,106 @@ public class DfsGarbageCollectorTest {
 		}
 	}
 
+	@Test
+	public void reftableWithoutTombstoneResurrected() throws Exception {
+		RevCommit commit0 = commit().message("0").create();
+		String NEXT = "refs/heads/next";
+		DfsRefDatabase refdb = (DfsRefDatabase)repo.getRefDatabase();
+		git.update(NEXT, commit0);
+		Ref next = refdb.exactRef(NEXT);
+		assertNotNull(next);
+		assertEquals(commit0, next.getObjectId());
+
+		git.delete(NEXT);
+		refdb.clearCache();
+		assertNull(refdb.exactRef(NEXT));
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		gc.setIncludeDeletes(false);
+		gc.setConvertToReftable(false);
+		run(gc);
+		assertEquals(1, odb.getReftables().length);
+		try (DfsReader ctx = odb.newReader();
+			 ReftableReader rr = odb.getReftables()[0].open(ctx)) {
+			rr.setIncludeDeletes(true);
+			assertEquals(1, rr.minUpdateIndex());
+			assertEquals(2, rr.maxUpdateIndex());
+			assertNull(rr.exactRef(NEXT));
+		}
+
+		RevCommit commit1 = commit().message("1").create();
+		DfsPackDescription t1 = odb.newPack(INSERT);
+		Ref newNext = new ObjectIdRef.PeeledNonTag(Ref.Storage.LOOSE, NEXT,
+				commit1);
+		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
+			ReftableWriter w = new ReftableWriter();
+			w.setMinUpdateIndex(1);
+			w.setMaxUpdateIndex(1);
+			w.begin(out);
+			w.writeRef(newNext, 1);
+			w.finish();
+			t1.addFileExt(REFTABLE);
+			t1.setReftableStats(w.getStats());
+		}
+		odb.commitPack(Collections.singleton(t1), null);
+		assertEquals(2, odb.getReftables().length);
+		refdb.clearCache();
+		newNext = refdb.exactRef(NEXT);
+		assertNotNull(newNext);
+		assertEquals(commit1, newNext.getObjectId());
+	}
+
+	@Test
+	public void reftableWithTombstoneNotResurrected() throws Exception {
+		RevCommit commit0 = commit().message("0").create();
+		String NEXT = "refs/heads/next";
+		DfsRefDatabase refdb = (DfsRefDatabase)repo.getRefDatabase();
+		git.update(NEXT, commit0);
+		Ref next = refdb.exactRef(NEXT);
+		assertNotNull(next);
+		assertEquals(commit0, next.getObjectId());
+
+		git.delete(NEXT);
+		refdb.clearCache();
+		assertNull(refdb.exactRef(NEXT));
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		gc.setIncludeDeletes(true);
+		gc.setConvertToReftable(false);
+		run(gc);
+		assertEquals(1, odb.getReftables().length);
+		try (DfsReader ctx = odb.newReader();
+			 ReftableReader rr = odb.getReftables()[0].open(ctx)) {
+			rr.setIncludeDeletes(true);
+			assertEquals(1, rr.minUpdateIndex());
+			assertEquals(2, rr.maxUpdateIndex());
+			next = rr.exactRef(NEXT);
+			assertNotNull(next);
+			assertNull(next.getObjectId());
+		}
+
+		RevCommit commit1 = commit().message("1").create();
+		DfsPackDescription t1 = odb.newPack(INSERT);
+		Ref newNext = new ObjectIdRef.PeeledNonTag(Ref.Storage.LOOSE, NEXT,
+				commit1);
+		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
+			ReftableWriter w = new ReftableWriter();
+			w.setMinUpdateIndex(1);
+			w.setMaxUpdateIndex(1);
+			w.begin(out);
+			w.writeRef(newNext, 1);
+			w.finish();
+			t1.addFileExt(REFTABLE);
+			t1.setReftableStats(w.getStats());
+		}
+		odb.commitPack(Collections.singleton(t1), null);
+		assertEquals(2, odb.getReftables().length);
+		refdb.clearCache();
+		assertNull(refdb.exactRef(NEXT));
+	}
+
 	private TestRepository<InMemoryRepository>.CommitBuilder commit() {
 		return git.commit();
 	}

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

@@ -108,6 +108,7 @@ public class DfsGarbageCollector {
 	private PackConfig packConfig;
 	private ReftableConfig reftableConfig;
 	private boolean convertToReftable = true;
+	private boolean includeDeletes;
 	private long reftableInitialMinUpdateIndex = 1;
 	private long reftableInitialMaxUpdateIndex = 1;
 
@@ -185,6 +186,17 @@ public class DfsGarbageCollector {
 		return this;
 	}
 
+	/**
+	 * @param include
+	 *            if true, the garbage collector will include tombstones for
+	 *            deleted references in the reftable. Default is {@code false}.
+	 * @return {@code this}
+	 */
+	public DfsGarbageCollector setIncludeDeletes(boolean include) {
+		includeDeletes = include;
+		return this;
+	}
+
 	/**
 	 * Set minUpdateIndex for the initial reftable created during conversion.
 	 *
@@ -699,7 +711,7 @@ public class DfsGarbageCollector {
 		try (ReftableStack stack = ReftableStack.open(ctx, reftablesBefore)) {
 			ReftableCompactor compact = new ReftableCompactor();
 			compact.addAll(stack.readers());
-			compact.setIncludeDeletes(false);
+			compact.setIncludeDeletes(includeDeletes);
 			compactReftable(pack, compact);
 		}
 	}

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

@@ -438,6 +438,7 @@ public class ReftableBatchRefUpdate extends BatchRefUpdate {
 
 		ReftableCompactor compactor = new ReftableCompactor();
 		compactor.setConfig(cfg);
+		compactor.setIncludeDeletes(true);
 		compactor.addAll(tables);
 		compactor.compact(out);
 		return compactor.getStats();