checkpoint: collapse GitStore constructors into NewGitStore(repo, refs)

Every callsite now passes the resolved CommittedRefs (or DefaultV1Refs in tests). The GitStore stores the full topology, not just a read ref. promoteRemoteTrackingMetadataBranch is renamed to promoteRemoteTrackingPrimary; readCheckpointInfoFromRef and checkRemoteMetadata take CommittedRefs. The fallback-to-origin gate in getSessionsBranchTree and the resume bootstrap gate are both Read == Primary && PrimaryFetchableFromOrigin so the local-only mirror ref keeps skipping the remote-tracking fallback.