### Please describe the problem.
Git-annex with v6 repo causes weird file creation behavior.

### What steps will reproduce the problem?
On central repo:
  git init --bare central6
  cd central6
  git annex init origin
  git annex upgrade
On Client A
  git clone {central6 repo path/URI}
  cd central6
  git annex init clientA6
  git annex upgrade
On Client B
  git clone {central6 repo path/URI}
  cd central6
  git annex init clientB6
  git annex upgrade
Start assistant on both clients.
Start webapp on both clients.
Add files to both clients.
Wait for assistant to sync new files.
Force sync with webapp on both clients 

At this point examine files coming from the central repo on the non-originating client.  I see:
Client A originated file:
-rw-rw-r--. 1 user group 92528731 May 10 20:16 image.png
Client B created file:
-rw-rw-r--. 1 user group 103 May 10 20:21 image.png

Here's the content of Client B's file:
/annex/objects/SHA256E-s92528731--098928032fddbd0327c1d608249a133e276a00b8aa8bffca371bd32bded49777.png

### What version of git-annex are you using? On what operating system?
Linux (Fedora 23/CentOS 7)
[[!format sh """
git-annex version: 6.20160428-g1f253e8
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: 5 6
upgrade supported from repository versions: 0 1 2 4 5
"""]]

### Please provide any additional information below.

[[!format sh """
# Client B
[2016-05-10 20:09:51.879642] main: starting assistant version 6.20160428-g1f253e8
[2016-05-10 20:09:52.127709] Cronner: You should enable consistency checking to protect your data. 
[2016-05-10 20:09:57.340186] TransferScanner: Syncing with origin 
(scanning...) [2016-05-10 20:09:58.182781] Watcher: Performing startup scan
(started...) 

merge: refs/remotes/origin/master - not something we can merge

merge: refs/remotes/origin/synced/master - not something we can merge
gpg: Signature made Thu 28 Apr 2016 10:44:48 AM EDT using DSA key ID 89C809CB
gpg: /tmp/git-annex-gpg.tmpOTZtDq/trustdb.gpg: trustdb created
gpg: Good signature from "git-annex distribution signing key (for Joey Hess) <id@joeyh.name>"
gpg: WARNING: This key is not certified with a trusted signature!
gpg:          There is no indication that the signature belongs to the owner.
Primary key fingerprint: 4005 5C6A FD2D 526B 2961  E78F 5EE1 DBA7 89C8 09CB
git-annex: Daemon is already running.
[2016-05-10 20:21:19.633914] main: Syncing with origin 
From /smb/r7000/USB_Storage/tmp/git-annex/central6
   7f1d48c..3e6f240  git-annex  -> origin/git-annex
 * [new branch]      master     -> origin/master
 * [new branch]      synced/git-annex -> origin/synced/git-annex
 * [new branch]      synced/master -> origin/synced/master
(merging origin/git-annex into git-annex...)
(recording state in git...)

Already up-to-date.
[2016-05-10 20:21:23.337732] Pusher: Syncing with origin 
To /smb/r7000/USB_Storage/tmp/git-annex/central6
   3e6f240..358afc3  git-annex -> synced/git-annex
[2016-05-10 20:21:25.056294] Committer: Adding image.png
add image.png ok
[2016-05-10 20:21:25.543293] Committer: Committing changes to git
(recording state in git...)

SHA256E-s103--d7d52e9de4a9c7c030743825c3a1ca072062e4ccadefcf1eb34be3004360b9b2.png
            103 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=0/1)
(checksum...) [2016-05-10 20:21:27.240904] Transferrer: Uploaded image.png
[2016-05-10 20:21:27.787233] Pusher: Syncing with origin 
[2016-05-10 20:21:28.12119] Committer: Adding image.png
(recording state in git...)
add image.png ok
[2016-05-10 20:21:28.696135] Committer: Committing changes to git
(recording state in git...)
To /smb/r7000/USB_Storage/tmp/git-annex/central6
   358afc3..e3ef364  git-annex -> synced/git-annex
   15d9319..976e99f  master -> synced/master
[2016-05-10 20:21:32.584488] Pusher: Syncing with origin 
Everything up-to-date

# 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)
It seems to work really well on v5, but the file "corruption" is difficult to recover from.