### Please describe the problem.
While running git annex sync, it may failed if one did run it on some deep directory, and the sync remove this direcory.

### What version of git-annex are you using? On what operating system?

git-annex version: 4.20130815
build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP
local repository version: 3
default repository version: 3
supported repository versions: 3 4
upgrade supported from repository versions: 0 1 2

on Debian Gnu Linux sid

> [[fixed|done]] --[[Joey]]
