[[!comment format=mdwn username="joey" subject="""comment 2""" date="2016-04-14T16:59:40Z" content=""" I've fixed this bug. After upgrading to git-annex 6.20160414 or newer, if you have such files in your repository, you will need to force git-annex to update its list of unlocked files, by running: git annex init --version=6 You may also need to run `git annex fsck` on the files to properly populate them with their content. Do it after the above command. (There were also some bugs that lost the execute bit; fixed those too.) (The comment about windows is not about this bug at all, but an entirely different, and already fixed bug.) """]]