### Please describe the problem.
Incorrect merge of direct repos.

### What steps will reproduce the problem?

[[!format sh """
# setting up stuff
test/a$ git init
test/a$ git annex init
test/a$ git annex direct
test/a$ touch firstfile
test/a$ git annex add firstfile
$ git clone test/a
$ mv a test/b
test/b$ git annex direct

# actual scenario
test/b$ echo bbbb > f
test/b$ git annex add f
test/b$ git annex sync
test/a$ mkdir f
test/a$ echo aaaa > f/f
test/a$ git annex add f/f
test/a$ git annex sync
test/b$ git annex sync
test/b$ rm f
test/b$ git annex sync
test/b$ ls
test/b$ firstfile
test/b$ f.variant-SHA256E-s5--4551db5fd4d56e27be71a8a943070cfaa4342b8e960a326e2d6427b3aa0a5a48.variant-43f5
test/a$ git annex sync  # A's f/f is no longer to be found
"""]]

### What version of git-annex are you using? On what operating system?
[[!format sh """
git-annex version: 4.20131031-g7d99d14
build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi TDFA CryptoHash
key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
remote types: git gcrypt S3 bup directory rsync web webdav glacier hook

Linux ceilingcat 3.11.6-1-ARCH #1 SMP PREEMPT Fri Oct 18 23:22:36 CEST 2013 x86_64 GNU/Linux
"""]]

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