### Please describe the problem.
git annex status returns:

annexed files in working tree: fatal: git ls-files: cannot generate relative filenames containing '..'

There are unlocked files mixed with locked (symlinked) throughout the repository after a commit. 
Perhaps my repo is in an inconsistent state?

### What steps will reproduce the problem?
Run git annex status

### What version of git-annex are you using? On what operating system?
git-annex version: 4.20131106.  Redhat EL6 running on KVM.

### 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
[username@box pnt]$ git annex status
repository mode: indirect
trusted repositories: 0
semitrusted repositories: 2
        00000000-0000-0000-0000-000000000001 -- web
        1ff41d2d-02bd-4795-88b9-bf3fbbeabef7 -- here
untrusted repositories: 0
transfers in progress: none
available local disk space: 36.86 terabytes (+1 megabyte reserved)
local annex keys: 35750
local annex size: 251.11 gigabytes
annexed files in working tree: fatal: git ls-files: cannot generate relative filenames containing '..'
0
size of annexed files in working tree: 0 bytes
bloom filter size: 16 mebibytes (7.2% full)
backend usage: 
        SHA256: 18471
        SHA256E: 17279
[username@box pnt]$ git annex version
git-annex version: 4.20131106
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
local repository version: 3
default repository version: 3
supported repository versions: 3 4
upgrade supported from repository versions: 0 1 2

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

> Added note about git version to from scratch installation instructions.
> Debian package already depends on a newer version. [[done]] --[[Joey]]
