don't count clusters as copies, continued

don't count clusters as copies, continued

Handled limitCopies, as well as everything using fromNumCopies and
fromMinCopies.

This should be everything, probably.

Note that, git-annex info displays a count of repositories, which still
includes cluster. I think that's ok. It would be possible to filter out
clusters there, but to the user they're pretty much just another
repository. The numcopies displayed by eg `git-annex info .` does not
include clusters.