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.