fix annex.skipunknown false error propagation

Propagate nonzero exit status from git ls-files when a specified file does
not exist, or a specified directory does not contain any files checked into
git.

The recent completion of the annex.skipunknown transition exposed this
bug, that has unfortunately been lurking all along.

It is also possible that git ls-files errors out for some other reason
-- perhaps a permission problem -- and this will also fix error propagation
in such situations.

Sponsored-by: Dartmouth College's Datalad project