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/tooling.py

@@ -0,0 +1,13 @@
+"""Tooling helpers extracted from the duplex pipeline."""
+
+from __future__ import annotations
+
+from typing import Any
+
+
+def normalize_tool_name(name: Any, aliases: dict[str, str]) -> str:
+    """Normalize tool name with alias mapping."""
+    normalized = str(name or "").strip()
+    if not normalized:
+        return ""
+    return aliases.get(normalized, normalized)