"unknown transitions listed in local; upgrade git-annex!" I'm not sure what is happening anymore. I disabled the assistant so I can set up what I wanted to exclude from certain repositories, after which I decided to just not use the assistant. Started working per usual with my repositories and now this error appears: unknown transitions listed in local; upgrade git-annex! This appears whenever I use `enableremote`, `fsck`, `get`, `move`, `drop`, and others. I've checked the source of this line, but I don't know what it means.

Apparently the problem was that somehow the git tree for 3 of my 4 repositories was... incomplete? If I removed all remotes but my bup repository the message disappeared but `git annex sync` still failed with a "fatal: refusing to merge unrelated histories", which should have been fixed in April. I decided using `git fetch --all` for all repositories, manually merged with the `--allow-unrelated-histories` option, uninit'ed all the repositories and rebuilt them from scratch. The "fatal: refusing to merge unrelated histories" appeared again since I have several disconnected repositories with more or less the same set of files but I knew how to resolve that.