git annex - how to verify 2 repositories are exactly identical

How can I ensure that when I clone, sync, and get content from another git annex repository that I have setup an identical mirror? I have used a tool like unison in the past which did a file to file comparison, but that is time and memory intensive. Are there any other alternatives so I can perform a sanity check? The main motivation for this is that I just made a clone of an existing repository it is smaller. I expect it to be smaller because the old repository has unused or unreferenced objects, but it is quite a bit different in size. So, I'd like to have some check I can run.