### Please describe the problem.
Using the webapp to generate a new (local) repository instantly takes it to the following state:
[[!format sh """
user@local:~/Annex$ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#	deleted:    uuid.log
#
user@local:~/Annex$ git branch
  git-annex
* master
user@local:~/Annex$ git log
commit 90bfcaf17b0576d8ecdc48ae44dda22d41464acc
Author: local  <user>
Date:   Sun Nov 3 15:30:17 2013 +0100

    created repository
user@local:~/Annex$ git show HEAD
commit 90bfcaf17b0576d8ecdc48ae44dda22d41464acc
Author: local  <user>
Date:   Sun Nov 3 15:30:17 2013 +0100

    created repository

diff --git a/uuid.log b/uuid.log
new file mode 100644
index 0000000..9df3670
--- /dev/null
+++ b/uuid.log
@@ -0,0 +1 @@
+987e7b9a-aa9d-41db-ae92-23fcae7f6187 user@local:~/Annex timestamp=1383489017.181
user@local:~/Annex$ 
"""]]

I'm new to git-annex, so I'm not quite sure, but looking at [[internals]] this file should only exist in the git-annex branch, not in master. Furthermore, from this state it seems impossible to get "sync with your other devices" to work, because of a merge conflict on this change.

Perhaps some sort of a race-condition with the annex-assistant picking up the uuid.log file while the repository is being initialized?

### What version of git-annex are you using? On what operating system?
Ubuntu 13.10 with git-annex 4.20130815

> [[fixed|done]]; see comments. (This fix needs to be backported to Ubuntu.) --[[Joey]]