fix(e2e): pin git-branch when E2E_CHECKPOINT_STORE is unset

With the store unset (local test:e2e:canary / test:ci / check), TestMain left ENTIRE_CHECKPOINTS_PRIMARY unset, so first-run enable wrote git-refs while the harness's backend-aware assertions still defaulted to the v1 branch — every branch-shaped assertion timed out. Pin git-branch when unset; the env also suppresses the first-run settings write.

Trail-Finding: 019f712a-a2ad-7c38-ba73-074d9eb55c85