What steps will reproduce the problem?

I don't know how, but this happened already a second time, I don't know how to reproduce this yet.

What is the expected output? What do you see instead?

There are many three character name directories created that look like the parts of a hash - and each contains a logfile.

% ls
027
1d1
1e3
232
36e
583
5f6
69c
9ea
bd7
c46
d20
d48
f31
f88
uuid.log
[+the intended data directories]

% find 027/
027/
027//b73
027//b73/SHA256-s10108928--3c3766aed8b66de9d0ef37820e0ddfba25f9463b37f30e25ceb5ce3cdf12db36.log

 % cat f88/7c3/SHA256-s4100608--903530747dfdc7bc9d487d7cbd8ab09ddc1ffad52c08849d049c8a5ff5cfb854.log
1351711677.187589s 1 2efd46d2-0e32-11e2-95fe-f73f09c6615e
1351971337.667243s 1 ab50cd8a-11c0-11e2-934c-87e45f64e5c6

What version of git-annex are you using? On what operating system?

% git-annex version git-annex version: 3.20121017 local repository version: 3 default repository version: 3 supported repository versions: 3 upgrade supported from repository versions: 0 1 2

OS X 10.6.8

Please provide any additional information below.

I use a symlink to the repository to change into it.

The three character directories, as well as the uuid.log file are supposed to stay in the git-annex branch. Perhaps you have somehow merged that branch into your master branch? I recommend you look at the history of your git repository to see how it happened. It seems very unlikely that git-annex did this.
Comment by http://joeyh.name/ Sat Nov 10 00:36:49 2012
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