diff --git a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
index 421fa8a..cf190a6 100644
--- a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
@@ -29,6 +29,7 @@
  org.eclipse.jgit.internal;version="[4.9.0,4.10.0)",
  org.eclipse.jgit.internal.storage.dfs;version="[4.9.0,4.10.0)",
  org.eclipse.jgit.internal.storage.file;version="[4.9.0,4.10.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[4.9.0,4.10.0)",
  org.eclipse.jgit.junit;version="[4.9.0,4.10.0)",
  org.eclipse.jgit.junit.http;version="[4.9.0,4.10.0)",
  org.eclipse.jgit.lib;version="[4.9.0,4.10.0)",
diff --git a/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/RefsUnreadableInMemoryRepository.java b/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/RefsUnreadableInMemoryRepository.java
index a1e41d1..21787fe 100644
--- a/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/RefsUnreadableInMemoryRepository.java
+++ b/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/RefsUnreadableInMemoryRepository.java
@@ -46,6 +46,7 @@
 
 import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
 import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
+import org.eclipse.jgit.internal.storage.reftable.Reftable;
 import org.eclipse.jgit.lib.RefDatabase;
 
 /**
@@ -80,14 +81,12 @@
 	}
 
 	private class RefsUnreadableRefDatabase extends MemRefDatabase {
-
 		@Override
-		protected RefCache scanAllRefs() throws IOException {
+		protected Reftable read() throws IOException {
 			if (failing) {
 				throw new IOException("disk failed, no refs found");
-			} else {
-				return super.scanAllRefs();
 			}
+			return super.read();
 		}
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
index bb6017c..fd727ae 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
@@ -14,7 +14,6 @@
 import static org.junit.Assert.fail;
 
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.concurrent.TimeUnit;
 
@@ -714,38 +713,6 @@
 	}
 
 	@Test
-	public void leavesNonGcReftablesIfNotConfigured() throws Exception {
-		String master = "refs/heads/master";
-		RevCommit commit0 = commit().message("0").create();
-		RevCommit commit1 = commit().message("1").parent(commit0).create();
-		git.update(master, commit1);
-
-		DfsPackDescription t1 = odb.newPack(INSERT);
-		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
-			out.write("ignored".getBytes(StandardCharsets.UTF_8));
-			t1.addFileExt(REFTABLE);
-		}
-		odb.commitPack(Collections.singleton(t1), null);
-
-		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
-		gc.setReftableConfig(null);
-		run(gc);
-
-		// Single GC pack present with all objects.
-		assertEquals(1, odb.getPacks().length);
-		DfsPackFile pack = odb.getPacks()[0];
-		DfsPackDescription desc = pack.getPackDescription();
-		assertEquals(GC, desc.getPackSource());
-		assertTrue("commit0 in pack", isObjectInPack(commit0, pack));
-		assertTrue("commit1 in pack", isObjectInPack(commit1, pack));
-
-		// Only INSERT REFTABLE above is present.
-		DfsReftable[] tables = odb.getReftables();
-		assertEquals(1, tables.length);
-		assertEquals(t1, tables[0].getPackDescription());
-	}
-
-	@Test
 	public void prunesNonGcReftables() throws Exception {
 		String master = "refs/heads/master";
 		RevCommit commit0 = commit().message("0").create();
@@ -754,7 +721,7 @@
 
 		DfsPackDescription t1 = odb.newPack(INSERT);
 		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
-			out.write("ignored".getBytes(StandardCharsets.UTF_8));
+			new ReftableWriter().begin(out).finish();
 			t1.addFileExt(REFTABLE);
 		}
 		odb.commitPack(Collections.singleton(t1), null);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
index 6e9d7e0..d568d72 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
@@ -446,7 +446,7 @@
 				// add, as the pack was already committed via commitPack().
 				// If this is the case return without changing the list.
 				for (DfsPackFile p : o.packs) {
-					if (p == newPack)
+					if (p.key.equals(newPack.key))
 						return;
 				}
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
index 383ed3d..0bb4e30 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
@@ -6,30 +6,12 @@
 import java.nio.ByteBuffer;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.ConcurrentMap;
 import java.util.concurrent.atomic.AtomicInteger;
-import java.util.concurrent.locks.ReadWriteLock;
-import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
-import org.eclipse.jgit.lib.BatchRefUpdate;
-import org.eclipse.jgit.lib.ObjectId;
-import org.eclipse.jgit.lib.ObjectIdRef;
-import org.eclipse.jgit.lib.ProgressMonitor;
-import org.eclipse.jgit.lib.Ref;
-import org.eclipse.jgit.lib.Ref.Storage;
 import org.eclipse.jgit.lib.RefDatabase;
-import org.eclipse.jgit.revwalk.RevObject;
-import org.eclipse.jgit.revwalk.RevTag;
-import org.eclipse.jgit.revwalk.RevWalk;
-import org.eclipse.jgit.transport.ReceiveCommand;
-import org.eclipse.jgit.util.RefList;
 
 /**
  * Git repository stored entirely in the local process memory.
@@ -54,9 +36,8 @@
 	static final AtomicInteger packId = new AtomicInteger();
 
 	private final MemObjDatabase objdb;
-	private final RefDatabase refdb;
+	private final MemRefDatabase refdb;
 	private String gitwebDescription;
-	private boolean performsAtomicTransactions = true;
 
 	/**
 	 * Initialize a new in-memory repository.
@@ -92,7 +73,7 @@
 	 * @param atomic
 	 */
 	public void setPerformsAtomicTransactions(boolean atomic) {
-		performsAtomicTransactions = atomic;
+		refdb.performsAtomicTransactions = atomic;
 	}
 
 	@Override
@@ -148,6 +129,7 @@
 			if (replace != null)
 				n.removeAll(replace);
 			packs = n;
+			clearCache();
 		}
 
 		@Override
@@ -159,37 +141,43 @@
 		protected ReadableChannel openFile(DfsPackDescription desc, PackExt ext)
 				throws FileNotFoundException, IOException {
 			MemPack memPack = (MemPack) desc;
-			byte[] file = memPack.fileMap.get(ext);
+			byte[] file = memPack.get(ext);
 			if (file == null)
 				throw new FileNotFoundException(desc.getFileName(ext));
 			return new ByteArrayReadableChannel(file, blockSize);
 		}
 
 		@Override
-		protected DfsOutputStream writeFile(
-				DfsPackDescription desc, final PackExt ext) throws IOException {
-			final MemPack memPack = (MemPack) desc;
+		protected DfsOutputStream writeFile(DfsPackDescription desc,
+				PackExt ext) throws IOException {
+			MemPack memPack = (MemPack) desc;
 			return new Out() {
 				@Override
 				public void flush() {
-					memPack.fileMap.put(ext, getData());
+					memPack.put(ext, getData());
 				}
 			};
 		}
 	}
 
 	private static class MemPack extends DfsPackDescription {
-		final Map<PackExt, byte[]>
-				fileMap = new HashMap<>();
+		final byte[][] fileMap = new byte[PackExt.values().length][];
 
 		MemPack(String name, DfsRepositoryDescription repoDesc) {
 			super(repoDesc, name);
 		}
+
+		void put(PackExt ext, byte[] data) {
+			fileMap[ext.getPosition()] = data;
+		}
+
+		byte[] get(PackExt ext) {
+			return fileMap[ext.getPosition()];
+		}
 	}
 
 	private abstract static class Out extends DfsOutputStream {
 		private final ByteArrayOutputStream dst = new ByteArrayOutputStream();
-
 		private byte[] data;
 
 		@Override
@@ -221,7 +209,6 @@
 		public void close() {
 			flush();
 		}
-
 	}
 
 	private static class ByteArrayReadableChannel implements ReadableChannel {
@@ -281,19 +268,11 @@
 		}
 	}
 
-	/**
-	 * A ref database storing all refs in-memory.
-	 * <p>
-	 * This class is protected (and not private) to facilitate testing using
-	 * subclasses of InMemoryRepository.
-	 */
-    protected class MemRefDatabase extends DfsRefDatabase {
-		private final ConcurrentMap<String, Ref> refs = new ConcurrentHashMap<>();
-		private final ReadWriteLock lock = new ReentrantReadWriteLock(true /* fair */);
+	/** DfsRefDatabase used by InMemoryRepository. */
+	protected class MemRefDatabase extends DfsReftableDatabase {
+		boolean performsAtomicTransactions = true;
 
-		/**
-		 * Initialize a new in-memory ref database.
-		 */
+		/** Initialize a new in-memory ref database. */
 		protected MemRefDatabase() {
 			super(InMemoryRepository.this);
 		}
@@ -302,172 +281,5 @@
 		public boolean performsAtomicTransactions() {
 			return performsAtomicTransactions;
 		}
-
-		@Override
-		public BatchRefUpdate newBatchUpdate() {
-			return new BatchRefUpdate(this) {
-				@Override
-				public void execute(RevWalk walk, ProgressMonitor monitor)
-						throws IOException {
-					if (performsAtomicTransactions() && isAtomic()) {
-						try {
-							lock.writeLock().lock();
-							batch(getCommands());
-						} finally {
-							lock.writeLock().unlock();
-						}
-					} else {
-						super.execute(walk, monitor);
-					}
-				}
-			};
-		}
-
-		@Override
-		protected RefCache scanAllRefs() throws IOException {
-			RefList.Builder<Ref> ids = new RefList.Builder<>();
-			RefList.Builder<Ref> sym = new RefList.Builder<>();
-			try {
-				lock.readLock().lock();
-				for (Ref ref : refs.values()) {
-					if (ref.isSymbolic())
-						sym.add(ref);
-					ids.add(ref);
-				}
-			} finally {
-				lock.readLock().unlock();
-			}
-			ids.sort();
-			sym.sort();
-			objdb.getCurrentPackList().markDirty();
-			return new RefCache(ids.toRefList(), sym.toRefList());
-		}
-
-		private void batch(List<ReceiveCommand> cmds) {
-			// Validate that the target exists in a new RevWalk, as the RevWalk
-			// from the RefUpdate might be reading back unflushed objects.
-			Map<ObjectId, ObjectId> peeled = new HashMap<>();
-			try (RevWalk rw = new RevWalk(getRepository())) {
-				for (ReceiveCommand c : cmds) {
-					if (c.getResult() != ReceiveCommand.Result.NOT_ATTEMPTED) {
-						ReceiveCommand.abort(cmds);
-						return;
-					}
-
-					if (!ObjectId.zeroId().equals(c.getNewId())) {
-						try {
-							RevObject o = rw.parseAny(c.getNewId());
-							if (o instanceof RevTag) {
-								peeled.put(o, rw.peel(o).copy());
-							}
-						} catch (IOException e) {
-							c.setResult(ReceiveCommand.Result.REJECTED_MISSING_OBJECT);
-							ReceiveCommand.abort(cmds);
-							return;
-						}
-					}
-				}
-			}
-
-			// Check all references conform to expected old value.
-			for (ReceiveCommand c : cmds) {
-				Ref r = refs.get(c.getRefName());
-				if (r == null) {
-					if (c.getType() != ReceiveCommand.Type.CREATE) {
-						c.setResult(ReceiveCommand.Result.LOCK_FAILURE);
-						ReceiveCommand.abort(cmds);
-						return;
-					}
-				} else {
-					ObjectId objectId = r.getObjectId();
-					if (r.isSymbolic() || objectId == null
-							|| !objectId.equals(c.getOldId())) {
-						c.setResult(ReceiveCommand.Result.LOCK_FAILURE);
-						ReceiveCommand.abort(cmds);
-						return;
-					}
-				}
-			}
-
-			// Write references.
-			for (ReceiveCommand c : cmds) {
-				if (c.getType() == ReceiveCommand.Type.DELETE) {
-					refs.remove(c.getRefName());
-					c.setResult(ReceiveCommand.Result.OK);
-					continue;
-				}
-
-				ObjectId p = peeled.get(c.getNewId());
-				Ref r;
-				if (p != null) {
-					r = new ObjectIdRef.PeeledTag(Storage.PACKED,
-							c.getRefName(), c.getNewId(), p);
-				} else {
-					r = new ObjectIdRef.PeeledNonTag(Storage.PACKED,
-							c.getRefName(), c.getNewId());
-				}
-				refs.put(r.getName(), r);
-				c.setResult(ReceiveCommand.Result.OK);
-			}
-			clearCache();
-		}
-
-		@Override
-		protected boolean compareAndPut(Ref oldRef, Ref newRef)
-				throws IOException {
-			try {
-				lock.writeLock().lock();
-				ObjectId id = newRef.getObjectId();
-				if (id != null) {
-					try (RevWalk rw = new RevWalk(getRepository())) {
-						// Validate that the target exists in a new RevWalk, as the RevWalk
-						// from the RefUpdate might be reading back unflushed objects.
-						rw.parseAny(id);
-					}
-				}
-				String name = newRef.getName();
-				if (oldRef == null)
-					return refs.putIfAbsent(name, newRef) == null;
-
-				Ref cur = refs.get(name);
-				if (cur != null) {
-					if (eq(cur, oldRef))
-						return refs.replace(name, cur, newRef);
-				}
-
-				if (oldRef.getStorage() == Storage.NEW)
-					return refs.putIfAbsent(name, newRef) == null;
-
-				return false;
-			} finally {
-				lock.writeLock().unlock();
-			}
-		}
-
-		@Override
-		protected boolean compareAndRemove(Ref oldRef) throws IOException {
-			try {
-				lock.writeLock().lock();
-				String name = oldRef.getName();
-				Ref cur = refs.get(name);
-				if (cur != null && eq(cur, oldRef))
-					return refs.remove(name, cur);
-				else
-					return false;
-			} finally {
-				lock.writeLock().unlock();
-			}
-		}
-
-		private boolean eq(Ref a, Ref b) {
-			if (!Objects.equals(a.getName(), b.getName()))
-				return false;
-			if (a.isSymbolic() != b.isSymbolic())
-				return false;
-			if (a.isSymbolic())
-				return Objects.equals(a.getTarget().getName(), b.getTarget().getName());
-			else
-				return Objects.equals(a.getObjectId(), b.getObjectId());
-		}
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
index fa2e8a9..8731aab 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
@@ -117,6 +117,10 @@
 
 		Config cfg = refdb.getRepository().getConfig();
 		reftableConfig = new ReftableConfig();
+		if (refdb instanceof InMemoryRepository.MemRefDatabase) {
+			reftableConfig.setAlignBlocks(false);
+			reftableConfig.setIndexObjects(false);
+		}
 		reftableConfig.fromConfig(cfg);
 	}