refactor: type discovery core

[jackwener]

Summary

• tighten typing across manifest building, CLI discovery, validation, and Commander bridging
• replace broad any usage with explicit YAML/manifest shape types and shared error helpers
• keep runtime behavior unchanged while shrinking the discovery-layer loose typing surface

Validation

• npm run typecheck
• npm run build
• npx vitest run src/build-manifest.test.ts src/engine.test.ts