phases: always write with a repo In the future change that move the internal representation of phase-roots from node-id to rev-num, we will use a repository to translate revision numbers back to node at write time. Since that future change is quite complicated already, we do this small API change beforehand.

phases: mark `phasecache.phaseroots` private We are about to change its content from nodeid to revnum. So anyone directly using the content might be in unexpected troubles. We start by making it private to explicitly break any such user (and discourage them to do so).