refactor(core): centralize config, purify domain, and modernize LLM adapters

[4nibhal]

Summary

• centralize runtime config resolution across API, CLI, and container wiring
• remove filesystem I/O from domain indexing policies
• make src/ and tests/ pass current Ruff/mypy expectations
• replace prompt-centric LLM generation with a message-oriented port
• add OpenAI-compatible provider alias support and base URL forwarding
• normalize test packaging and lint-driven hygiene cleanup

Architecture

This PR consolidates several related modernization steps that were previously coupled by the same runtime seams:

• Config architecture

  • BhodiConfig now owns API transport settings through ApiConfig
  • API and CLI entrypoints consume resolved config instead of rebuilding it ad hoc
  • indexing compatibility settings now flow through the central config path

• Domain purity

  • indexing rules no longer inspect the filesystem directly
  • domain policy checks now operate on supplied facts (IndexingTarget) instead of concrete path I/O

• LLM architecture

  • generate_with_context is removed entirely
  • the LLM port is now message-oriented
  • RAG context assembly moves into the application layer, so adapters only translate canonical messages to provider calls

• Provider-family direction

  • OpenAI-family adapters now support compatible endpoints via alias resolution and base_url
  • credential injection remains at the composition boundary

• Quality posture

  • product source is now green under mypy src/
  • repo tests are green under ruff check tests/

Testing

• uv run ruff check src tests
• uv run mypy src/
• uv run pytest

Results:

• Ruff ✅
• mypy ✅
• pytest ✅ 261 passed

Notes

• No AIWF/OpenCode behavior changes are included in this PR.
• Remaining warnings are upstream/dependency warnings from Starlette TestClient and OpenTelemetry.