[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="64.134.31.139"
 subject="comment 3"
 date="2013-10-16T20:45:25Z"
 content="""
At least part of this sounds like [[direct_mode_assistant_in_subdir_confusion]]. The report is too confused for me to tell if that's the whole of the problem.

Note that git-annex stores files in git, so if it did something wrong, you can switch to indirect mode, and use regular git commands to check out a tree from before the problem occurred.
"""]]