(refactor): RAG prototype composition and CLI runtime wiring

[Intrinsical-AI]

Summary

This PR updates RAG prototype composition and runtime wiring with backend-aware container setup, refactors CLI command responsibilities, hardens settings/runtime behavior, and refreshes operational docs for provider contracts.

Scope

• Adds backend-aware composition wiring in adapters/container.
• Extracts reusable helpers for eval CLI flow.
• Improves index CLI status output and guard checks.
• Normalizes settings flow and hardens MCP/runtime outputs.
• Updates provider/API contract documentation.

Validation

• UV_CACHE_DIR=/tmp/uv_cache uv run ruff format --check .
• UV_CACHE_DIR=/tmp/uv_cache uv run ruff check .
• UV_CACHE_DIR=/tmp/uv_cache uv run mypy src
• UV_CACHE_DIR=/tmp/uv_cache uv run pytest -q

Commit sequence

1. refactor(rag): add backend-aware composition wiring
2. refactor(rag): extract eval CLI helpers
3. refactor(rag): improve CLI status output and guards
4. fix(rag): normalize settings and harden runtime outputs
5. docs(rag): update provider and API contract docs