strategy: finish refs.Primary migration

Remaining v1-pinned production sites move to refs.Primary: GetRemoteMetadataBranchTree becomes GetRemotePrimaryTree; trailer formatters in manual_commit_logs.go use Primary's short name; ListTemporary filters out the primary ref when it's a branch; DeleteOrphanedCheckpoints, IsMetadataDisconnected, WarnIfMetadataDisconnected, ReconcileDisconnectedMetadataBranch, and doctor's disconnected-metadata check all consult refs.Primary and gate remote-tracking work on PrimaryFetchableFromOrigin. The only remaining paths.MetadataBranchName uses in production are the resolver itself and IsShadowBranch's structural v1 filter.