A couple times working in an annex manually, I accidentally did "git add" instead of "git annex add" and ended up with files checked into my repo instead of symlinks. So now there is some file content in git, rather than in the annex. Is there any way to root that out, or is it there forever? (My limited knowledge of git says: it's there forever, unless maybe you go into the branches where it lives, do an interactive rebase to the time before it was added, remove that commit, replay history, and then garbage collect, but I have no idea if that would suddenly break git annex, and it sounds painful anyway.)
If say I were a neat freak and wanted to just start over with a clean annex, I imagine the thing to do would be to just start the hell over -- and if I wanted to do that, the way to go would be to get into a full repository, do a "git annex uninit" and then throw away the .git directory, then do "git init" and "git annex init" and then "git annex add ." ?