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_dynamic_variables.py

@@ -1,4 +1,4 @@
-from core.session import Session
+from runtime.session.manager import Session
 
 
 def _session() -> Session: