Added a comment: this just happened to me as well
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[[!comment format=mdwn
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username="https://www.google.com/accounts/o8/id?id=AItOawn9JRcJ_69McoLFe5-dvTMdfS9rJpGy6JI"
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nickname="Warren"
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subject="this just happened to me as well"
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date="2013-03-29T23:28:05Z"
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content="""
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I was trying to undo some changes from another bare repo, and then all of a sudden the three letter directories popped up. I think the way I did this was to hard reset the master and git-annex branches to the same commit. I take it that was the wrong thing to do? I take it the git-annex and master branch should never be merged?
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"""]]
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