fix(config): support split output directories and native contracts

[Kentakoong]

Summary

• add independent project-relative functionsDir and typesDir source options while preserving the existing colocated default
• resolve the nearest ancestor tsconfig that defines usable paths, so split output trees use configured aliases instead of deep relative imports
• colocate custom base.ts output with the generated type root
• preserve native request contracts, concrete response types, DELETE bodies, required query parameters, and TanStack mutation parameters
• wrap only operations matching the primary response envelope, preserve operation-specific envelope fields, and leave differently shaped data envelopes untouched
• generate valid array, union, query-parameter, and Tiptap contracts

Verification

• pnpm verify
• 56 test files / 302 tests passed
• coverage: 96.73% statements, 90.47% branches, 99.57% functions
• split-layout integration fixture verifies @mirai/utils/... runtime imports and @mirai/types/... type imports with no deep relative paths
• strict generated-project typechecking covers native query, mutation, body, and response contracts