The code used to rely on the clone code calling the remote's save, which
does not happen anymore, meaning that the configuration settings the
remote expected were not being written to disk.

The run-time configuration was still being affected, so the right branch
was being cloned. The tests continued to pass as we did not check for
the configuration entires. Fix this by creating the remote with the
single-branch refspec we want and checking for its existence in the
configuration.