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/terminal.nix

@@ -1,10 +1,10 @@
 {
   imports = [
-    ../../apps/neovim/neovim.nix
-    ../../apps/git/home.nix
-    ../../apps/zoxide/home.nix
-    ../../apps/fish/home.nix
-    ../../apps/ghostty/home.nix
-    ../../apps/fastfetch/home.nix
+    ../../apps/neovim
+    ../../apps/git
+    ../../apps/zoxide
+    ../../apps/fish
+    ../../apps/ghostty
+    ../../apps/fastfetch
   ];
 }