P1: add project lifecycle commands

[lzehrung]

Summary

• add init/status/sync/uninit lifecycle commands backed by .codegraph/manifest.json
• track file signatures, config/build-option drift, cache warmup, and safe uninit behavior
• document lifecycle root semantics and update the Codegraph skill

Verification

• rtk npm run build
• rtk npx vitest run tests/lifecycle.test.ts
• rtk npm run check
• ODW review-and-correct review plus verify-fixes rounds: final verify resolved 1/1 prior finding with 0 unresolved and 0 regressions