[[!comment format=mdwn
 username="joey"
 subject="""comment 9"""
 date="2015-10-19T17:37:32Z"
 content="""
git init will never create a bare git repository (unless you specify
--bare), and a normal bare repository doesn't have a .git directory.

So I suspect that your repository is using git-annex's direct
mode, which only sets core.bare as an implementation detail. Likely
you trimmed off the end of the .git/config, where it said "direct = true"
"""]]
