@highco I ran into this same issue and ended up solving by using the Merge.merge function instead of Merge.commits. One problem that took me a while to track down is that you need to specify Checkout.STRATEGY.FORCE (or some other non-default strategy) or else it won't change your working directory you'll end up with a completely empty merge commit.

Here's a code snippet that hopefully is helpful:

async function createMergeCommit(repo, otherCommit, mergeMessage) {
  const annotatedCommit = await nodegit.AnnotatedCommit.lookup(repo, otherCommit.id());
  await nodegit.Merge.merge(repo, annotatedCommit, null, {
    checkoutStrategy: nodegit.Checkout.STRATEGY.FORCE,
  });
  const index = await repo.refreshIndex();
  if (index.hasConflicts()) {
    throw new CLIError('Unexpected conflict when creating merge commit.');
  }
  await index.write();
  const treeOid = await index.writeTree();
  await repo.createCommit(
    'HEAD',
    repo.defaultSignature(),
    repo.defaultSignature(),
    mergeMessage,
    treeOid,
    [await repo.getHeadCommit(), otherCommit]
  );
  repo.stateCleanup();
}

Full example here:
https://github.com/alangpierce/bulk-decaffeinate/blob/master/src/land.js

Writing index after merge throws error #1128

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