refactor: implement component-based architecture for enhanced maintainability

- Reorganize directory structure into core/, features/, and themes/
- Colocate application Nix logic, configs, scripts, and theme overrides
- Implement 'Inversion of Control' for theming: apps now pull theme-specific layouts
- Update flake.nix and shared library paths to match the new structure
- Document the new Feature-Centric architecture in README.md

themes/engine/scripts/nomarchy-theme-refresh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# Refresh the current theme from its templates.
+
+THEME_NAME_PATH="$HOME/.config/nomarchy/current/theme.name"
+
+if [[ -f $THEME_NAME_PATH ]]; then
+  nomarchy-theme-set "$(cat $THEME_NAME_PATH)"
+fi