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_tool_executor.py

@@ -1,6 +1,6 @@
 import pytest
 
-from core.tool_executor import execute_server_tool
+from tools.executor import execute_server_tool
 
 
 @pytest.mark.asyncio
@@ -38,7 +38,7 @@ async def test_current_time_uses_local_system_clock(monkeypatch):
     async def _should_not_be_called(_tool_id):
         raise AssertionError("fetch_tool_resource should not be called for current_time")
 
-    monkeypatch.setattr("core.tool_executor.fetch_tool_resource", _should_not_be_called)
+    monkeypatch.setattr("tools.executor.fetch_tool_resource", _should_not_be_called)
 
     result = await execute_server_tool(
         {