fix(strategy): heal pre-existing empty orphan metadata ref via checkpoint_remote

EnsurePrimaryRef only attempted the checkpoint_remote bootstrap fetch when the local primary ref was missing entirely. A repo that already had a local empty orphan on entire/checkpoints/v1 (the exact shape left behind by a pre-#1374 entire enable) and whose origin doesn't track Primary (the checkpoint_remote strategy) returned early without ever trying to recover the real branch, so re-running enable after upgrading left the repo permanently stuck on the empty orphan.