test(integration): fix false-positive in clone graceful-degradation test

Root-caused the git-refs KNOWN BUG skip: it was a harness artifact, not a backend divergence. The test staged the session's file changes after the stop hook, so the "no files modified during session" gate skipped condensation on BOTH backends. git-branch still passed only because the assertion (v1 branch exists) was satisfied by the checkpoint inherited from origin via the plain clone; git-refs correctly reported no local checkpoint (per-checkpoint refs are not fetched by a default clone).

Stage before stop like a real agent session (and like the createCheckpointedCommit helper), drop the skip, and assert a NEW checkpoint ID was condensed so inherited clone data can never satisfy the check again.