### Please describe the problem.
Shortly after starting the assistant the local client repository is in an inconsistent state. Just using the cli works fine without destroying the repository.

### What steps will reproduce the problem?
- Working git annex repository

- Start the Git-Annex Assistant
> git annex assistant

- Wait a short time and then check the repository state:
> ➜  annex git:(master) ✗ gst
> On branch master
> error: Could not read ea63b58d1252e3432280cdce1282eb02035c926e
> error: Could not read ea63b58d1252e3432280cdce1282eb02035c926e
> fatal: Failed to traverse parents of commit 108fa97a989aeabff16738558e1aa636c836598b

- refs/heads/synced/git-annex links to an unknown commit
> ➜  .git git:(master) cat refs/heads/synced/git-annex
> be8e6023fbb172b12cec8fdbaa8654194f71c4f5% 

> git show be8e6023fbb172b12cec8fdbaa8654194f71c4f5
> fatal: unable to read source tree (d2959525362dcadd4dbec96a8f18d80cc689a851)

### What version of git-annex are you using? On what operating system?
- git-annex version: 5.20150508-gf71c23f
- Mac OSX 10.10.2

### Please provide any additional information below.

[[!format sh """

[2015-05-15 07:06:32 CEST] main: starting assistant version 5.20150508-gf71c23f
[2015-05-15 07:06:32 CEST] Cronner: Consistency check in progress
fsck 2015-05-01 07.56.02.jpg (checksum…)
ok
fsck 2015-05-01 09.55.58.jpg (checksum…)
ok
fsck 2015-05-14 12.38.24.jpg (checksum…)
ok
fsck 2015-05-14 12.39.30.jpg (checksum…)
ok
fsck 2015-05-14 12.40.49.jpg (checksum…)
ok
fsck 2015-05-14 12.40.53.jpg (checksum…)
ok
fsck 2015-05-14 12.43.42.jpg (checksum…)
ok
fsck 2015-05-14 12.44.16.jpg (checksum…)
ok
fsck 2015-05-14 12.45.11.jpg (checksum…)
ok
(recording state in git…)
[2015-05-15 07:06:39 CEST] TransferScanner: Syncing with nas 
(scanning…) [2015-05-15 07:06:39 CEST] Watcher: Performing startup scan
gpg: Unterschrift vom Fr  8 Mai 22:10:28 2015 CEST mittels DSA-Schlüssel ID 89C809CB
gpg: Unterschrift kann nicht geprüft werden: Öffentlicher Schlüssel nicht gefunden
(started…) 
[2015-05-15 07:06:41 CEST] Committer: Committing changes to git
(recording state in git…)
[2015-05-15 07:06:41 CEST] Pusher: Syncing with nas 


0%            0.0 B/s 0s
2%          32.0KB/s 47s
...
90%         467.6KB/s 0s
                        
[2015-05-15 07:06:47 CEST] Transferrer: Uploaded 2015-05-1..38.24.jpg


0%            0.0 B/s 0s
1%          32.0KB/s 54s
...
91%         534.5KB/s 0s
                        
[2015-05-15 07:06:54 CEST] Transferrer: Uploaded 2015-05-1..45.11.jpg


0%            0.0 B/s 0s
2%        16.0KB/s 1m30s
…
90%         440.4KB/s 0s
                        
[2015-05-15 07:07:01 CEST] Transferrer: Uploaded 2015-05-1..44.16.jpg


0%            0.0 B/s 0s
1%        16.0KB/s 1m42s
...
91%         508.2KB/s 0s
                        
[2015-05-15 07:07:07 CEST] Transferrer: Uploaded 2015-05-1..43.42.jpg


0%            0.0 B/s 0s
1%        16.0KB/s 1m40s
...
91%         371.6KB/s 0s
                        
[2015-05-15 07:07:13 CEST] Transferrer: Uploaded 2015-05-1..40.53.jpg


0%            0.0 B/s 0s
1%          32.0KB/s 50s
...
91%         495.1KB/s 0s
                        
[2015-05-15 07:07:19 CEST] Transferrer: Uploaded 2015-05-1..40.49.jpg


0%            0.0 B/s 0s
1%          32.0KB/s 53s
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92%         528.2KB/s 0s
                        
[2015-05-15 07:07:25 CEST] Transferrer: Uploaded 2015-05-1..39.30.jpg
ssh: connect to host 1.2.3.43 port 22: Operation timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: ‚/Volumes/WD1500GB/annex‘ does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
ssh: connect to host 1.2.3.43 port 22: Operation timed out
s(recording state in git…)
fatal: ‚/Volumes/WD1500GB/annex‘ does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
ssh: connect to host 1.2.3.43 port 22: Operation timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
[2015-05-15 07:08:16 CEST] Cronner: Attempting to repair aether [here]
Unpacking all pack files.
ssh: connect to host 1.2.3.43 port 22: Operation timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
ssh: connect to host 1.2.3.36 port 22:sssssh: connect to host 1.2.3.43 port 22: Operation timed out
fatal: early EOF


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