Add comprehensive inline documentation to all modules and enhance README

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

templates/rde/overlays/python.nix

@@ -1,7 +1,22 @@
 # Python packages overlay
+#
+# This overlay configures the Python environment with essential packages.
+# Note: Most Python packages should be managed via uv (pyproject.toml)
+# This overlay is for packages needed at the system level.
+#
+# Usage:
+#   - Add system-level Python packages to the list below
+#   - For project-specific packages, use uv (e.g., 'uv add package-name')
+#   - The Python interpreter is available via pkgs.python
+#
+# Example additions:
+#   - numpy, pandas, scipy for scientific computing
+#   - pytest, black, mypy for development tools
 final: prev: {
+  # Python 3 with system-level packages
   python = prev.python3.withPackages (pyPackages:
     with pyPackages; [
-      requests
+      requests  # HTTP library for making API calls
+      # Add more system-level packages here
     ]);
 }