### Please describe the problem.
One of my annexes has duplicate entries in one of the older trees. This causes git-annex repair to attempt to repair it.

### What version of git-annex are you using? On what operating system?
6.20161027-g27d824e (standalone x86_64 tarball) on ArchLinux latest as of 29th of Oct 2016 x86_64.

### Please provide any additional information below.

[[!format sh """
[0 zerodogg@firefly annexed]$ git annex version
git-annex version: 6.20161027-g27d824e
build flags: Assistant Webapp Pairing Testsuite S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external
local repository version: 6
supported repository versions: 3 5 6
upgrade supported from repository versions: 0 1 2 3 4 5
operating system: linux x86_64
[0 zerodogg@firefly annexed]$ git annex info                             
repository mode: indirect
trusted repositories: 0
semitrusted repositories: 23
# …snip
untrusted repositories: 0
transfers in progress: none
available local disk space: 47.89 gigabytes (+500 megabytes reserved)
local annex keys: 2300
local annex size: 1.72 gigabytes
annexed files in working tree: 2492
size of annexed files in working tree: 1.89 gigabytes
bloom filter size: 32 mebibytes (0.5% full)
backend usage:
        SHA256E: 2492
[0 zerodogg@firefly annexed]$ git fsck
Checking object directories: 100% (256/256), done.
error in tree 3818a8ea201197ed355aa87133a718afca7c4a49: duplicateEntries: contains duplicate file entries
error in tree 255f43cff847013439117a3fc4cfa517a90f38cb: duplicateEntries: contains duplicate file entries
error in tree 404b4124800ece4772296d1f7559d982d0bc4cbd: duplicateEntries: contains duplicate file entries
Checking objects: 100% (334784/334784), done.
Checking connectivity: 334784, done.
[4 zerodogg@firefly annexed]$ git annex repair -d
Running git fsck ...
[2016-10-29 09:55:24.652234] read: git ["--version"]
[2016-10-29 09:55:24.668729] process done ExitSuccess
[2016-10-29 09:55:24.668879] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","fsck","--no-dangling","--no-reflogs"]
[2016-10-29 09:55:34.306776] process done ExitFailure 4
Unpacking all pack files.
[2016-10-29 09:55:34.307446] call: mv ["-f",".git/objects/pack/pack-18d920ca3181f59af68dc6b0061ca2430884a9bb.pack","/tmp/packsFokxCF/pack-18d920ca3181f59af68dc6b0061ca243
0884a9bb.pack1804289383846930886.tmp"]
[2016-10-29 09:55:34.334238] process done ExitSuccess
[2016-10-29 09:55:34.336992] feed: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","unpack-objects","-r"]
Unpacking objects: 100% (334784/334784), done.
[2016-10-29 09:56:39.505888] process done ExitSuccess
[2016-10-29 09:56:39.560473] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show","10c1cc2127a7be7cf3ce4a0d69ed53e4c375f888"]
[2016-10-29 09:56:39.607717] process done ExitSuccess
# ^C
# End of transcript or log.
"""]]

### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
I use it for everything, around 3TB of data at the moment. It is awesome.
