Program: 113200
Project: 113200
Buggy source:
private void updateRefs(){
  final Optional<Ref> currHead=command(RefParse.class).setName(Ref.HEAD).call();
  final String currentBranch;
  if (currHead.isPresent() && currHead.get() instanceof SymRef) {
    currentBranch=((SymRef)currHead.get()).getTarget();
  }
 else {
    currentBranch="String_Node_Str";
  }
  ImmutableSet<Ref> changedRefs=getChangedRefs();
  try {
    refDatabase().lock();
  }
 catch (  TimeoutException e) {
    Throwables.propagate(e);
  }
  try {
    for (    Ref ref : changedRefs) {
      if (!ref.getName().startsWith(Ref.REFS_PREFIX)) {
        continue;
      }
      Ref updatedRef=ref;
      Optional<Ref> repoRef=command(RefParse.class).setName(ref.getName()).call();
      if (repoRef.isPresent() && repositoryChanged(repoRef.get())) {
        if (rebase) {
          transaction.command(CheckoutOp.class).setSource(ref.getName()).setForce(true).call();
          try {
            transaction.command(RebaseOp.class).setUpstream(Suppliers.ofInstance(repoRef.get().getObjectId())).call();
          }
 catch (          RebaseConflictsException e) {
            Throwables.propagate(e);
          }
          updatedRef=transaction.command(RefParse.class).setName(ref.getName()).call().get();
        }
 else {
          transaction.command(CheckoutOp.class).setSource(ref.getName()).setForce(true).call();
          try {
            transaction.command(MergeOp.class).setAuthor(authorName.orNull(),authorEmail.orNull()).addCommit(repoRef.get().getObjectId()).call();
          }
 catch (          NothingToCommitException e) {
          }
          updatedRef=transaction.command(RefParse.class).setName(ref.getName()).call().get();
        }
      }
      LOGGER.debug(String.format("String_Node_Str",ref.getName(),ref.getObjectId(),updatedRef.getObjectId()));
      command(UpdateRef.class).setName(ref.getName()).setNewValue(updatedRef.getObjectId()).call();
      if (currentBranch.equals(ref.getName())) {
        command(UpdateSymRef.class).setName(Ref.HEAD).setNewValue(ref.getName()).call();
        command(UpdateRef.class).setName(Ref.WORK_HEAD).setNewValue(updatedRef.getObjectId()).call();
        command(UpdateRef.class).setName(Ref.STAGE_HEAD).setNewValue(updatedRef.getObjectId()).call();
      }
    }
  }
  finally {
    refDatabase().unlock();
  }
}

Fixed version (ground truth):
private void updateRefs(){
  final Optional<Ref> currHead=command(RefParse.class).setName(Ref.HEAD).call();
  final String currentBranch;
  if (currHead.isPresent() && currHead.get() instanceof SymRef) {
    currentBranch=((SymRef)currHead.get()).getTarget();
  }
 else {
    currentBranch="String_Node_Str";
  }
  List<ChangedRef> changedRefs=getChangedRefs();
  try {
    refDatabase().lock();
  }
 catch (  TimeoutException e) {
    Throwables.propagate(e);
  }
  try {
    for (    ChangedRef change : changedRefs) {
      final String refName=change.name;
      if (!refName.startsWith(Ref.REFS_PREFIX)) {
        continue;
      }
      final boolean isDelete=change.newValue == null;
      final boolean isNew=change.orignalValue == null;
      final ObjectId oldCommit=isNew ? null : ObjectId.valueOf(change.orignalValue);
      final ObjectId newCommit=isDelete ? null : ObjectId.valueOf(change.newValue);
      final Optional<Ref> currentRef=command(RefParse.class).setName(refName).call();
      final Ref updatedRef;
      if (currentRef.isPresent() && repositoryChanged(currentRef.get())) {
        if (rebase) {
          transaction.command(CheckoutOp.class).setSource(refName).setForce(true).call();
          try {
            transaction.command(RebaseOp.class).setUpstream(Suppliers.ofInstance(currentRef.get().getObjectId())).call();
          }
 catch (          RebaseConflictsException e) {
            Throwables.propagate(e);
          }
          updatedRef=transaction.command(RefParse.class).setName(refName).call().get();
        }
 else {
          transaction.command(CheckoutOp.class).setSource(refName).setForce(true).call();
          try {
            transaction.command(MergeOp.class).setAuthor(authorName.orNull(),authorEmail.orNull()).addCommit(currentRef.get().getObjectId()).call();
          }
 catch (          NothingToCommitException e) {
          }
          updatedRef=transaction.command(RefParse.class).setName(refName).call().get();
        }
      }
 else {
        updatedRef=isDelete ? null : new Ref(refName,newCommit);
      }
      LOGGER.debug(String.format("String_Node_Str",refName,oldCommit,newCommit));
      command(UpdateRef.class).setName(refName).setNewValue(updatedRef == null ? null : updatedRef.getObjectId()).setDelete(isDelete).call();
      if (currentBranch.equals(refName)) {
        command(UpdateSymRef.class).setName(Ref.HEAD).setNewValue(refName).call();
        command(UpdateRef.class).setName(Ref.WORK_HEAD).setNewValue(updatedRef.getObjectId()).call();
        command(UpdateRef.class).setName(Ref.STAGE_HEAD).setNewValue(updatedRef.getObjectId()).call();
      }
    }
  }
  finally {
    refDatabase().unlock();
  }
}