[[!comment format=mdwn username="joey" subject="""comment 2""" date="2015-06-09T19:34:57Z" content=""" So, thanks for providing me the index file, but the relevant problem seems to be that your index file refers to a git object that failed to make it to disk. The most likely cause of this would be a crash before disk buffers got flushed, or something like that. It's perfectly fine to remove your .git/annex/index if this happens. You must have lost some information that was being committed to the git-annex branch, so you might want to run `git annex fsck` to make sure everything gets updated. I'd expect `git-annex repair` to detect this problem (and fix it the same way you did). It's possible that the assistant's code for detecting when there are problems doesn't work well enough for it to have automatically detected and fixed this problem. Which is why I'm leaving this bug open for now. """]]