Re-organize Nix Modules

- Move all programs into system folder
- Create `default.nix` for each folder to reduce number of imports
  in configuration.nix
- Rename some modules to be more generic and less package
  specific to allow for easy swapping of programs in the future
- Update flake.lock

system/gui/gnome.nix

@@ -2,7 +2,7 @@
 
 {
   imports = [
-    ./x11.nix
+    ./default.nix
   ];
 
   services.xserver.displayManager.gdm.enable = true;