It would be nice if git-annex could be used in bare git repos.
However, that is not currently supported. Problems include:

* git-annex often does not read a git repo's config before touching it,
  so it doesn't know if the repo is bare or not
  (reading the config when operating on ssh repos would be a pain and SLOW;
  I had some of that code in as of 1aa19422ac8748eeff219ac4f46df166dae783c5,
  but ripped it all out)
* .. which results in creating `.git/annex` in a bare repo, which mightily
  confuses git (so it will complain that the bare repo is not
  a git repo at all!)
* `.git-annex/` needs to have state recorded to it and committed, and that
  is not possible with a bare repo. (If [[todo/branching]] were done,
  that might be fixed.)