Files that have been deleted but not staged are being listed by git-annex commands. This is a recent reversion.

Does not seem to be due to the changes to how ls-files is used, as the old way also listed deleted files -- how did they get filtered out before and why did it break? --Joey

It's from 88a7fb5cbb7358f8d395f6c306fb9e94e1f1a724. Things used to use whenAnnexed, which uses lookupKey, which checks doesFileExist, so deleted files were filtered out there. So seekFilteredKeys should also check that.

Also, there should be a test case for this, IIRC there was one past case of a bug involving this and it's a bit of an easy edge case to forget about. --Joey