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

core/system/scripts/nomarchy-system-reboot

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Reboot command that first closes all application windows (thus giving them a chance to save state).
+# This is particularly helpful for applications like Chromium that otherwise won't shutdown cleanly.
+
+nomarchy-state clear re*-required
+
+# Schedule the reboot to happen after closing windows (detached from terminal)
+nohup bash -c "sleep 2 && systemctl reboot --no-wall" >/dev/null 2>&1 &
+
+# Now close all windows
+nomarchy-hyprland-window-close-all
+sleep 1 # Allow apps like Chrome to shutdown correctly