refactor: restore root layout and split mysql config

tools/project_layout.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python3
+"""Shared path helpers for the project layout."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+WORKSPACE_ROOT = PROJECT_ROOT / "workspace"