A common complaint is that git annex fsck in a bare repository complains about missing content of deleted files. That's because in a bare repository, git-annex operates on all versions of all files. Today I added a --branch option, so if you only want to check say, the master branch, you can: git annex fsck --branch master

The new option has other uses too. Want to get all the files in the v1.0 tag? git annex get --branch v1.0

It might be worth revisiting the implicit --all behavior for bare repositories. It could instead default to --branch HEAD or something like that. But I'd only want to change that if there was a strong consensus in favor.

Over 3/4th of the time spent implementing --branch was spent in adjusting the output of commands, to show "branch:file" is being operated on. How annoying.