refactor: standardize config structure and consolidate modules

- Standardized apps/ directory by renaming all entry points (e.g., home.nix) to default.nix and updating imports to use directory paths.
- Consolidated system/ logic into modules/system/, eliminating the top-level system/ directory and redundant wrappers.
- Merged subsidiary utility scripts (e.g., hakase-popup.nix, switch-wallpaper.nix) into their parent default.nix files for better cohesion.
- Cleaned up unused files and updated all module references to reflect the new structure.

modules/system/default.nix

@@ -1,20 +1,20 @@
 {pkgs, ...}: {
   imports = [
-    ../../system/time.nix
-    ../../system/nix.nix
-    ../../system/backlight.nix
-    ../../system/boot.nix
-    ../../system/amd.nix
-    ../../system/hardware.nix
-    ../../system/home-manager.nix
-    ../../system/services.nix
-    ../../system/user.nix
-    ../../system/version.nix
-    ../../system/fonts.nix
-    ../../system/programs.nix
-    ../../system/security.nix
-    ../../system/variables.nix
-    ../../system/kernel.nix
+    ./time.nix
+    ./nix.nix
+    ./backlight.nix
+    ./boot.nix
+    ./amd.nix
+    ./hardware.nix
+    ./home-manager.nix
+    ./services.nix
+    ./user.nix
+    ./version.nix
+    ./fonts.nix
+    ./programs.nix
+    ./security.nix
+    ./variables.nix
+    ./kernel.nix
   ];
   environment.systemPackages = with pkgs; [
     # FIXME: must be on their own app