refactor(api): split routes and system boundaries

[hanityx]

Summary

• Split API routes into provider, thread, and system route groups.
• Keep route index files as thin composers.
• Align recovery/system API boundaries with the domain split.

Stack

Base: PR 2 provider policy and safety split.
Next: runtime regressions and QA gates.

Validation

• Full stack validation previously run: corepack pnpm qa:provider PASS, corepack pnpm qa:pr PASS.
• Final hygiene pass after docs/test fixture cleanup: api-ts tests 43 files / 273 tests PASS, TUI tests 69 PASS, public markdown hygiene PASS.