feat: support .ignore overrides for indexing

[woshinibabuxuchongfu-maker]

Closes #699

Summary

• Load root .ignore after .gitignore so local negation patterns can re-include paths for CodeGraph indexing.
• Fall back to filesystem scanning when root .ignore exists, because git ls-files cannot see gitignored untracked files.
• Keep watcher filtering aligned with indexing behavior.
• Document .ignore as a local CodeGraph-only override layer.

Tests

• npx vitest run __tests__/extraction.test.ts -t "Directory Exclusion"
• npx vitest run __tests__/watcher.test.ts
• npm run build

Note: full npm test hit Windows temp cleanup EPERM errors and later worker OOM locally, unrelated to this change.