Activate substrate mutation controls

[heyoub]

Unproven first

• This closes only seven B2/B5 substrate evidence gaps selected from the 35 hosted survivors; it does not claim the remaining 28 are caught or that B3/B4 is closed.
• Hosted qualify, graph, and harness contexts are rerunning on the final review-fix head.
• Signal-only Git termination remains an explicit unexercised branch on Windows; the exact hosted polarity mutant is the ordinary nonzero-exit branch.

Exact basis

• base commit: a65dd13
• base tree: ee8fa1046bbce43da835a4e2d9f804b493c30e76
• head commit: 01ed15e
• head tree: 78986694607593e3f989fd9b63fb04e5aebf36fc

Claim

• Mutation campaign roots refuse before crossing process coordinates unless absolute.
• A failed Git cleanliness observation never becomes an empty clean listing.
• The final qualification Git read consumes the existing explicit-root Git command owner.
• Committed file counts are checked against a derived fixture population.
• Every bounded cat-file batch header field binds independently.
• The ordinary test subject root is checked by an independent coordinate derivation.
• Interrupted-run temp residue cannot preempt the Git-failure reversal.

Evidence

• cargo xtask qualify: 7/7 green on exact head 01ed15e.
• Focused targeted mutation campaign on 01ed15e: 7 examined, 7 caught, 0 missed, 0 timeout, 0 unviable.
• The typed mutation-report adapter reconciled the finalized structured report.
• Worktree clean after qualification and mutation.

Review disposition

• Greptile's temp-collision finding was valid and fixed in 01ed15e with bounded create-new retry and explicit cleanup.
• CodeRabbit produced no actionable finding.

Banked

• The obligation-join survivor belongs to B3/B4 and is not patched here.
• Equivalent/redundant mutations and the remaining reader/checker evidence gaps retain their prior dispositions; no broad survivor chase is implied.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 83206486-22d9-479f-a894-64ce130619d1

📥 Commits

Reviewing files that changed from the base of the PR and between a65dd13 and 7579b64.

📒 Files selected for processing (3)

• xtask/src/mutation_campaign.rs
• xtask/src/qualification.rs
• xtask/src/repository/snapshot.rs

Included review availability: Your plan includes up to 1 review per rolling hour; 0 remain after this review.

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📝 Walkthrough

Walkthrough

The changes harden repository-root and worktree validation, centralize Git command use, and extract git cat-file --batch header parsing. New tests cover invalid roots, failed Git status checks, malformed headers, and snapshot file counts.

Changes

Validation hardening

Layer / File(s)	Summary
Launcher repository-root validation xtask/src/mutation_campaign.rs	The mutation campaign launcher rejects relative repository roots and verifies the exact error message.
Worktree status validation xtask/src/qualification.rs	Worktree checks use the shared Git helper and return an error when Git status fails in a non-repository directory.
Batch header parsing and snapshot coverage xtask/src/repository/snapshot.rs	Batch-header parsing validates object identity, type, size, and extra fields. Tests cover malformed headers and snapshot file counts.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to 7579b

The PR adds targeted substrate mutation controls and validation checks, with the reported current-head qualification and mutation checks passing. No actionable merge-blocking risk remains after normal checks and review.

Possibly related PRs

• freebatteryfactory/ThreadPak#21: Related Git worktree and mutation-campaign validation changes.
• freebatteryfactory/ThreadPak#23: Related Git-backed snapshot and git cat-file --batch validation work.
• freebatteryfactory/ThreadPak#24: Related launcher and repository snapshot validation tests.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly describes the main objective: activating substrate mutation controls across the targeted qualification checks.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch phase5-survivor-controls

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