[[!comment format=mdwn username="http://joeyh.name/" ip="209.250.56.35" subject="comment 2" date="2014-01-06T16:14:29Z" content=""" As far as I can tell from git's code, this involves a \"cache-tree\" data structure stored in git's index file. git-annex has nothing to do with writing index files, beyond running git plumbing. So I don't see how this could be anything other than a corrupt index file (of a sort that git fsck doesn't detect), or a git bug. The best thing to do would be to send an example of a repository having this problem to the git developers for analysis. """]]