clone/update: include replace refs in clean mirrors

clone/update: include replace refs in clean mirrors

Although replace refs (see `git help replace`) may not be
commonly used, they can be shared and should any of the "clean"
refs use them, they need to be included.

Include the refs/replace/* namespace in the set of "clean refs"
when configuring a "clean" mirror.

As it's nontrivial to limit the replace refs to only those that
are actually used by the other "clean refs", this could end up
cloning extra stuff that is not logically part of a "clean" mirror.

This seems like a better solution than leaving them out since
that could result in a logically broken repository.

Signed-off-by: Kyle J. McKay <mackyle@gmail.com>