Fix sphinx complaints about the docs

Use the right namespace so Refspec and TransferProgress show up. These
classes are not instantiated by the user, so they were not promoted to
the pygit2 module. Use autoclass so it lists everything for us.

Also use autoclass for the reflog. We had a difference is oid vs id
between the docs and the code.
Merge remote-tracking branch 'carlos/doc-fixup'