[[!comment format=mdwn username="joey" subject="""@ben: what?""" date="2017-04-07T16:37:31Z" content=""" I don't know what you mean with `git annex init` in a v6 repo somehow doing something to a non-annexed file. That would be extemely surprising if it happened, and it does not happen when I try to follow your instructions. joey@darkstar:~/tmp/v62>git annex init --version=6 init (merging origin/git-annex into git-annex...) (recording state in git...) ok (recording state in git...) joey@darkstar:~/tmp/v62>ls x y@ joey@darkstar:~/tmp/v62>git annex get y get y (from origin...) (checksum...) ok (recording state in git...) joey@darkstar:~/tmp/v62>git status On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working tree clean """]]