I got the same error and couldn't solve it.
Then I noticed 3 extra files in one of my directories.
The files were named:
config, HEAD, description
I deleted the files, and the error didn't appear.
config
contained:
[core]
repositoryformatversion = 0
filemode = true
bare = true
HEAD
contained:
ref: refs/heads/master
description
contained:
Unnamed repository; edit this file 'description' to name the repository.