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 [[!commit 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]]

[[done]]
