Preserve ref tombstone when compact top retable stack

Change-Id: I07f5ad572b4642a7cdd76d92aa98f3b6c63d9fa2
Signed-off-by: Minh Thai <mthai@google.com>

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();