fix: tolerate doctor archive churn

[chubes4]

Summary

• Treat only ENOENT at the per-entry archive stat/header-read boundary as benign concurrent churn.
• Preserve inspection, malformed archive, I/O, permission, and archive-root enumeration failures instead of swallowing them.
• Keep existing checked/invalid semantics and add an aggregate skipped count without exposing vanished paths.
• Add deterministic regression coverage to the required check gate for post-enumeration disappearance and a still-present inspection error.

Root Cause

archiveCheck() enumerated archive paths and then called stat() and archive header validation without a per-entry disappearance boundary. A cache/runtime cleanup racing that inspection could remove an enumerated entry, allowing ENOENT to escape and replace the doctor report with wp-codebox/cli-failure/v1.

Error Boundary

inspectArchivePath() wraps only the individual entry's stat() and header read. ENOENT returns a skipped result; every other exception is rethrown. Root opendir() failures also remain surfaced.

Output Compatibility

The wp-codebox/doctor/v1 schema, statuses, messages, and existing checked/invalid fields are unchanged. Archive details gain only a numeric skipped field; vanished paths are not reported.

Verification

• npx tsx tests/doctor-archive-inspection.test.ts
• npx tsx scripts/doctor-command-smoke.ts
• npx tsc -b packages/cli --pretty false
• npm run build
• npm run check (102-command gate passed; Docker-dependent MySQL E2E explicitly skipped because Docker is unavailable)

No release or deployment occurred. No changelog, version, or generated release artifact was changed.

Fixes #2336