Refactor project structure and enhance backend integration

- Expanded package inclusion in `pyproject.toml` to support new modules.
- Introduced new `adapters` and `protocol` packages for better organization.
- Added backend adapter implementations for control plane integration.
- Updated main application imports to reflect new package structure.
- Removed deprecated core components and adjusted documentation accordingly.
- Enhanced architecture documentation to clarify the new runtime and integration layers.

engine/tests/test_backend_adapters.py

@@ -1,7 +1,7 @@
 import aiohttp
 import pytest
 
-from app.backend_adapters import (
+from adapters.control_plane.backend import (
     AssistantConfigSourceAdapter,
     LocalYamlAssistantConfigAdapter,
     build_backend_adapter,
@@ -120,7 +120,7 @@ async def test_http_backend_adapter_create_call_record_posts_expected_payload(mo
                 },
             )
 
-    monkeypatch.setattr("app.backend_adapters.aiohttp.ClientSession", _FakeClientSession)
+    monkeypatch.setattr("adapters.control_plane.backend.aiohttp.ClientSession", _FakeClientSession)
 
     config_dir = tmp_path / "assistants"
     config_dir.mkdir(parents=True, exist_ok=True)
@@ -198,7 +198,7 @@ async def test_with_backend_url_uses_backend_for_assistant_config(monkeypatch, t
             _ = (url, json)
             return _FakeResponse(status=200, payload={"id": "call_1"})
 
-    monkeypatch.setattr("app.backend_adapters.aiohttp.ClientSession", _FakeClientSession)
+    monkeypatch.setattr("adapters.control_plane.backend.aiohttp.ClientSession", _FakeClientSession)
 
     config_dir = tmp_path / "assistants"
     config_dir.mkdir(parents=True, exist_ok=True)
@@ -234,7 +234,7 @@ async def test_backend_mode_disabled_uses_local_assistant_config_even_with_url(m
             _ = timeout
             raise AssertionError("HTTP client should not be created when backend_mode=disabled")
 
-    monkeypatch.setattr("app.backend_adapters.aiohttp.ClientSession", _FailIfCalledClientSession)
+    monkeypatch.setattr("adapters.control_plane.backend.aiohttp.ClientSession", _FailIfCalledClientSession)
 
     config_dir = tmp_path / "assistants"
     config_dir.mkdir(parents=True, exist_ok=True)