When you rename, move or delete a folder (with files in it) the old folder doesn't get deleted in the other clients
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.
git annex sync
Please write back with a version number, and an example showing the problem happening.
I experienced this just now. Have a git-annex assistant repo set up (so using direct mode).
On one machine, I mv'd entire directories out of the git-annex repo.
The other machine saw the files deleted, but the directories remained.
On the machine on which I mv'd directories out, git-annex actually re-created some of them with symlinks to now-nonexistant hashes! I have no idea why it did that.