### Please describe the problem.

When cloning/syncing a repository (and probably doing some nono's in the process),
git annex will happily delete files.
This cost me several files, which just by coincidence were not totally important, still its *very* unsettling.

### What steps will reproduce the problem?

I did not try to exactly reproduce it yet (sorry, no time right now), but here is vaguley what I did (sorry its been a process spread over
several hours and i was doing lots of other things in parallel so I'm fuzzy about details):

 * have a repository in direct mode on your local harddrive, say ~/myannex
 * git clone ~/myannex to /usbhd/myannex, git annex init.
   The usbhd is a FAT, git annex recognizes it as "crippled filessytem".
 * Git annex get all from ~/myannex. So far, so good.
 * create several files on ~/myannex, git annex add them
 * do a git annex add on them, abort it (realizing SHA256E takes forever, so changing to WORM), repeat add
   (not sure wheter i did a git annex sync here)
 * create several files on /usbhd/myannex, git annex add them
   (not sure wheter i did a git annex sync here again)

All repos are in direct mode.

From here on i don't remember the exact order of events, one definite -- probably important -- nono i did,
was:
I executed a git annex sync/get on the usbhd in a sub-directory (i.e. not in the git base dir), say /usbhd/myannex/foo/bar/,
so it went on creating /usbhd/myannex/foo/bar/foo, which of course was not intended.
However /usbhd/myannex/foo/bar/foo contained FAT-crippled-symlinks to the new files in ~/myannex (good).

In order to avoid a potential messy situation i just renamed /usbhd/myannex/foo to /usbhd/myannex/foo_bak
(which I just realize while writing this, saved me the hash values of my files, yay :))

However when I tried to repeat the procedure, it seems that the new files would not appear on the usbhd (for a reason i totally don't get, maybe I synced back before realizing my sub-foo mistake).
When I synced usbhd -> ~/myannex again, git-annex happily deleted my new files there which obviously quite upset me.

Again, sorry for this horribly chaotic description,
I'll try and deliver a more reproducible description, but for the next 2 weeks at least I'm too busy for that.



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

Archlinux,
3.9.2-1-ARCH #1 SMP PREEMPT Sat May 11 20:31:08 CEST 2013 x86_64 GNU/Linux

aur/git-annex-bin 4.20131002-1

### Please provide any additional information below.

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log


# End of transcript or log.
"""]]

[[!tag moreinfo]]
