[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="209.250.56.2"
 subject="comment 1"
 date="2014-07-10T19:50:38Z"
 content="""
The files that you describe are normally tucked away on the git-annex branch of the git repository, where they're neither seen nor heard.

The most likely cause of your problem would be if you have done a \"git checkout git-annex\"  ... or worse, a \"git merge git-annex\".

So, check what branch you have checked out, and if it's the git-annex branch, you'll want to change back to master. If you've got master checked out and have these files, you can use `git log --stat` and see if there's a commit that added a bunch of these files to your master branch. Then you can revert that commit.
"""]]
