Work Packages: Root-vacuous chmod tests + TestOrdering isolation

Work Package WP01: Make the denied-write and ordering tests bite (#5654, #5186)

Dependencies: None

Requirement refs: FR-001, FR-002, FR-003, FR-004, FR-005, FR-006, SC-001, SC-002, SC-003

  • ✅ T001 Planted-break proof for the three read-only .gitignore sites and the two seam-injected sites (no test change)
  • ✅ T002 Seam-inject TestStoreUnreachable at the history-db open; prove it red against two planted breaks
  • ✅ T003 Delete GitignoreManager._atomic_write; retarget its two tests to write_gitignore_text; fix the read-only test docstring
  • ✅ T004 TestOrdering class-scoped autouse auto_discover_migrations() fixture; reproduce red first
  • ✅ T005 File the follow-up issue listing the remaining root-skipped chmod tests