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/home/apps.nix

@@ -1,8 +1,8 @@
 {
   imports = [
-    ../../apps/yazi/home.nix
-    ../../apps/gemini/home.nix
-    ../../apps/firefox/home.nix
-    # ../../apps/starship/home.nix
+    ../../apps/yazi
+    ../../apps/gemini
+    ../../apps/firefox
+    # ../../apps/starship
   ];
 }