PR #3479 fixed three false-positive classes in sdk/src/query/validate.ts but the fixes never propagated to get-shit-done/bin/lib/verify.cjs — the hand-maintained CJS runtime bundle that gsd-tools.cjs actually executes. W005: widened phase-dir regex from \d{2} to \d{2,} so 3+-digit prefixes like 999.1-foo are accepted. W006: adds forEachArchivedPhaseToken call after collectDiskPhases so phases whose directories live in a milestone archive are not flagged as missing. I001: adds canonicalPlanStem helper and uses it in summaryBases Set construction so 68-01-scaffolding-PLAN.md correctly matches 68-01-SUMMARY.md. Adds five regression tests (TDD red→green) covering each false-positive path. Fixes #3806 Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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