refactor: reorganize flake structure and consolidate user config

Directory structure:
- Move from src/ to root level (system/, user/)
- Remove unused machines (workstation, vm, laptop)

User configuration:
- Add user/home.nix for shared defaults (pass, essentials, default modules)
- Centralize user options in user/default.nix
- Move submodules to consistent paths (bash/bash, git/git, neovim/nvim, vim/vim)

Module reorganization:
- Flatten nested module structures (remove /modules/ subdirs)
- Split CLI vs GUI tools (dev/ for CLI, gui/dev/ for GUI)
- Move neovim/vim to top-level modules (not under utils/)
- Remove security.enable - pass now in user/home.nix
- Remove utils.enable - essentials now in user/home.nix
- Add security/yubikey module with yubikey-manager, age-plugin-yubikey
- Move pcb, design to gui/dev/
- Replace penpot docker wrapper with nixpkgs penpot-desktop
- Remove i3 config
- Remove deprecated wsl.nativeSystemd option

GUI improvements:
- Browser-focused mimeApps in gui/default.nix
- Each WM handles its own auto-start via profileExtra

Cleanup:
- Update README with new structure
- Update justfile paths and valid systems
- Fix submodule paths in .gitmodules

flake.nix

@@ -22,66 +22,36 @@
     };
   };
 
-  outputs = { nixpkgs, nur, home-manager, nixos-wsl, disko, ... }:
+  outputs = { nixpkgs, nur, ... }@inputs:
   let
-    system = "x86_64-linux";
-    pkgs = import nixpkgs {
+    mkPkgs = system: import nixpkgs {
       inherit system;
       config = {
         allowUnfree = true;
-	nvidia.acceptLicense = true;
+        nvidia.acceptLicense = true;
       };
       overlays = [
         nur.overlays.default
       ];
     };
 
+    mkSystem = { path, system ? "x86_64-linux" }:
+      let pkgs = mkPkgs system;
+      in nixpkgs.lib.nixosSystem {
+        inherit system pkgs;
+        specialArgs = { inherit inputs; };
+        modules = [ path ];
+      };
+
   in
-  with pkgs;
   {
     nixosConfigurations = {
-      desktop = nixpkgs.lib.nixosSystem {
-        inherit system pkgs;
-        modules = [
-          disko.nixosModules.disko
-          ./src/system/machines/desktop
-          home-manager.nixosModules.home-manager
-            (import ./src/system/machines/desktop/modules/home-manager)
-        ];
-      };
-
-      workstation = nixpkgs.lib.nixosSystem {
-        inherit system pkgs;
-        modules = [
-          ./src/system/machines/workstation
-          home-manager.nixosModules.home-manager
-            (import ./src/system/machines/workstation/modules/home-manager)
-        ];
-      };
-
-      server = nixpkgs.lib.nixosSystem {
-        inherit system pkgs;
-        modules = [
-          disko.nixosModules.disko
-          ./src/system/machines/server
-          home-manager.nixosModules.home-manager
-            (import ./src/system/machines/server/modules/home-manager)
-        ];
-      };
-
-      wsl = nixpkgs.lib.nixosSystem {
-        inherit system pkgs;
-        modules = [
-          ./src/system/machines/wsl
-          nixos-wsl.nixosModules.wsl
-            (import ./src/system/machines/wsl/modules/wsl)
-          home-manager.nixosModules.home-manager
-            (import ./src/system/machines/wsl/modules/home-manager)
-        ];
-      };
+      desktop = mkSystem { path = ./system/machines/desktop; };
+      server  = mkSystem { path = ./system/machines/server; };
+      wsl     = mkSystem { path = ./system/machines/wsl; };
     };
 
-    devShells.${system}.default = mkShell {
+    devShells.x86_64-linux.default = with mkPkgs "x86_64-linux"; mkShell {
       name = "devShell";
       packages = [
         just