fix(artifacts): prevent stale verifier evidence after scan

[pengfei-threemoonslab]

Summary

• treat the complete verifier control/identity surface as one lifecycle set when a standalone scan replaces a report
• remove stale verifier.json, handoff, PR comment, run projection, verification inputs, identity artifacts, receipt, and copied authorization before publishing the new report
• fail closed before replacing report.json when any stale verifier artifact cannot be removed, with an exact-path structured recovery action
• run baseline save's supporting scan in an isolated temporary directory so it cannot clobber the current report or forensic verifier evidence
• document command-scoped artifact authority, add the CHANGELOG entry, and regenerate llms-full.txt

Root cause

The original lifecycle set removed the terminal receipt and handoff but retained route-bearing surfaces such as verifier.json, verify-run.json, and pr-comment.md. That could leave a fresh standalone report.json beside an older actionable verifier route while deleting the receipt that made the mismatch detectable.

Separately, baseline save invoked run_scan without an explicit output directory. Its internal scan therefore used the manifest's normal reports directory, replacing report.json and triggering verifier cleanup even though the command only needed the in-memory report.

Impact

A standalone scan now retires all 11 verifier route/identity artifacts before publishing a replacement report. No stale control substrate or downstream feedback route survives beside a newer release decision. If cleanup is denied, the existing report remains untouched and agent mode names the exact file to remove.

baseline save now writes only the requested baseline/audit outputs; an existing verification receipt, handoff, verifier substrate, run projection, PR comment, inputs, and report remain byte-identical.

Validation

• focused regressions for scan cleanup, fail-closed recovery, preview → init → scan, baseline preservation, and verify rewrite ordering: passed
• full affected modules (test_scan.py, test_init_auto.py, test_cli.py, test_verify_orchestrator.py, test_baseline_integrity.py): 167 passed
• full repository suite: all non-packaging tests passed; the packaging fixture's isolated dependency install was blocked by the network sandbox, then all 8 packaging tests passed with package-index access
• Ruff checks for all modified Python files: passed
• git diff --check: passed
• Agents Shipgate committed-ref verify: control.state=complete, merge_verdict=mergeable, release decision passed, 0 blockers, 0 review items
• terminal verification receipt reproduced successfully

Closes #317