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/import_migration.md

@@ -0,0 +1,21 @@
+# Canonical Module Layout
+
+This MVP uses a single canonical module layout without legacy import shims.
+
+## Runtime and protocol
+
+- `protocol.ws_v1.schema`
+- `runtime.session.manager`
+- `runtime.pipeline.duplex`
+- `runtime.history.bridge`
+- `runtime.events`
+- `runtime.transports`
+- `runtime.conversation`
+- `runtime.ports.*`
+
+## Integrations and orchestration
+
+- `providers.*`
+- `adapters.control_plane.backend`
+- `workflow.runner`
+- `tools.executor`