Hello,
I'm trying to wrote a cronjob to fsck my git-annex bare repository on a server. My problem is that there are a lot of keys with no known copies because they were file that weren't meant to stay. So I want to only check files that are live in HEAD of master. Is there anyway to tell git-annex fsck to only check file that are used in some refs?
Thanks.

Currently the only way to do that is to make a clone of the bare repsitory that's not bare. Then run
git annex fsck --from origininside the clone. This is more efficient when the clone is on the same disk as the bare repository.Another way to deal with it is to use
git annex dead --keyto make fsk stop complaining about the specific keys that you don't mind are gone.It would be possible to add something like
git annex fsck --branch foowhich would operate on all files in the specified branch. I've opened ?operate on branch contents requesting that.