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/runtime/pipeline/llm_flow.py

@@ -0,0 +1,13 @@
+"""LLM flow helpers extracted from the duplex pipeline.
+
+This module is intentionally lightweight for phase-wise migration.
+"""
+
+from __future__ import annotations
+
+from providers.common.base import LLMStreamEvent
+
+
+def is_done_event(event: LLMStreamEvent) -> bool:
+    """Return whether an LLM stream event signals completion."""
+    return str(event.type) == "done"