git annex fsck --all was added, people
there's no way to stop it complaining about keys whose content is gone for
good. Well, there is now:
git annex dead --key can be used when you know
that a key is no longer available and want fsck to stop complaining about
Running fsck on a directory will intentionally still complain about files in the directory with missing contents, even if the keys have been marked dead.
The crucial part was finding a good way to store the information; luckily location log files are parsed in a way that lets it be added there without breaking backwards compatability. A bonus is that adding a key's content back to the annex will automatically bring it back from the dead.
I'm pondering making
git annex drop --force automatically mark a key as
dead when the last copy is dropped, but I don't know if it's too DWIM or
worth the complication. Another approach would be to let fsck mark keys as
dead, but that would certianly need an extra flag.