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/docs/extension_ports.md

@@ -4,31 +4,31 @@ This document defines the draft port set used to keep core runtime extensible.
 
 ## Port Modules
 
-- `core/ports/control_plane.py`
+- `runtime/ports/control_plane.py`
   - `AssistantRuntimeConfigProvider`
   - `ConversationHistoryStore`
   - `KnowledgeRetriever`
   - `ToolCatalog`
   - `ControlPlaneGateway`
-- `core/ports/llm.py`
+- `runtime/ports/llm.py`
   - `LLMServiceSpec`
   - `LLMPort`
   - optional extensions: `LLMCancellable`, `LLMRuntimeConfigurable`
-- `core/ports/tts.py`
+- `runtime/ports/tts.py`
   - `TTSServiceSpec`
   - `TTSPort`
-- `core/ports/asr.py`
+- `runtime/ports/asr.py`
   - `ASRServiceSpec`
   - `ASRPort`
   - optional extensions: `ASRInterimControl`, `ASRBufferControl`
-- `core/ports/service_factory.py`
+- `runtime/ports/service_factory.py`
   - `RealtimeServiceFactory`
 
 ## Adapter Layer
 
-- `app/service_factory.py` provides `DefaultRealtimeServiceFactory`.
+- `providers/factory/default.py` provides `DefaultRealtimeServiceFactory`.
 - It maps resolved provider specs to concrete adapters.
-- Core orchestration (`core/duplex_pipeline.py`) depends on the factory port/specs, not concrete provider classes.
+- Runtime orchestration (`runtime/pipeline/duplex.py`) depends on the factory port/specs, not concrete provider classes.
 
 ## Provider Behavior (Current)