[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="209.250.56.87"
 subject="comment 1"
 date="2013-12-12T19:16:34Z"
 content="""
I can't reproduce this. Tested in direct mode (which I assume you're using, but you didn't say), using both command-line `git annex sync`, and using the assistant. In all cases, when the last file in a directory was removed, the directory was deleted.

Please write back with a version number, and an example showing the problem happening.
"""]]