fix: align positional primary args and docs

[jackwener]

Summary

• convert a broad set of primary command inputs from named options to positional args
• keep manifest/discovery output aligned so packaged builds expose the same CLI shape
• refresh adapter docs and examples to match the updated command syntax

Validation

• npm run typecheck
• npm run build
• npx vitest run src/build-manifest.test.ts src/engine.test.ts
• custom manifest check for 27 positional command entries