Keep managed lineage runtime state invisible to Git

[Trecek]

Closes #5258

Managed headless launches currently leave lineage records visible to Git, so the clone gate can treat AutoSkillit's runtime state as user changes and refuse a clean checkout. This change gives the existing lineage namespace its own ignore marker, validates that marker before creating record directories, and repairs missing markers when a store operation reads an older namespace.

The temp directory and lineage store share the marker writer. Doctor and the root guards share the marker predicate; committed project directories are classified explicitly. Real-Git tests cover launch cleanliness, legacy repair, dispatch state, and continued detection of user edits. The static guard rejects unclassified .autoskillit children in production source.

Related issue: #5258. This PR remains draft pending the maintainer-owned policy registration.

Validation

• pre-commit run --all-files passed before each commit.
• Manual real-Git probe: before=[], after=[]; tracked ignore file unchanged; doctor OK.
• Mutation checks rejected both literal-root and root-variable path spellings; the temporary mutations were removed.
• Configured test_check (task test-local-gate) passed on 068f570b6: 47,307 passed, 610 skipped, 29 xfailed.
• The independent catalog row-count oracle is synchronized with the added guard row.
• core/io/io.py measures 749 non-import lines against its 750-line limit.

Historical prerequisites at this PR’s merge

A maintainer must add this prescribed entry to POLICY_SURFACES in tests/arch/_acceptance_policy_surfaces.py, then rerun the configured test_check gate after that policy change:

PolicySurface(
    "tests/arch/test_autoskillit_root_children_registered.py",
    "_CLASSIFIED_ELSEWHERE",
    "int_map",
    default=0,
),

The verified plan explicitly reserves that file for human edits, so it is unchanged in this PR. The post-merge E2E replay and PR #5255 commissioning remain operator-run checks. The three adjacent repairs were subsequently delivered together in #5263 without new trackers. The policy registration was subsequently merged in #5264; current clone-verification evidence is recorded in #5258.

Audit response

The audit's blocking REQ-006 finding used physical lines (wc -l) instead of the repository's defined budget count. tests/arch/_line_budget.py::count_budget_lines excludes import-statement spans, and scripts/check_file_lengths.py delegates to that function.

Revision	Physical lines	Excluded import lines	Enforced budget lines
Plan base 265f1e00e	766	23	743
PR implementation	772	23	749

The unchanged cap is 750 non-import lines. The plan's starting and final budget counts were correct, and its stop-and-report condition was not triggered. Direct check_file(io.py) returns no violation. No exemption, counter/cap change, unrelated trim, or module split was needed.

The three ODD test identifiers now exactly match the verified plan in 6194da647; their assertions and production behavior are unchanged. The gated rerun found one additional integration omission: the independent catalog-count oracle still expected the old table. 068f570b6 synchronizes that oracle while retaining its strict equality assertion, and the next full configured gate passed.

At this PR’s merge, E-3 and the policy registration were deferred. Those #5258 prerequisites have since been completed by #5264 and the two post-merge clone-admission replays recorded in #5258. Full #5255 commissioning still fails separately; no official re-audit GO is claimed.

Follow-up completion — 2026-10-11

#5263 completed the adjacent repairs, #5264 registered the restored policy map, and both post-merge default clone invocations succeeded in runs 38170521660 and 38170536595. See #5258 for the exact receipts and the separately failed full-commissioning outcomes.