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

user/home.nix

@@ -0,0 +1,38 @@
+{ lib, pkgs, config, ... }:
+
+let
+  pass = pkgs.pass.withExtensions (exts: with exts; [
+    pass-audit
+    pass-otp
+    pass-update
+    pass-tomb
+  ]);
+
+in
+{
+  programs.home-manager.enable = true;
+
+  home.username = config.user.name;
+  home.homeDirectory = "/home/${config.user.name}";
+
+  # Essential packages for all users
+  home.packages = with pkgs; [
+    pass
+    wget curl fastfetch fd
+    unzip zip rsync
+    calc calcurse
+  ];
+
+  programs.bash.shellAliases = {
+    cal = "${pkgs.calcurse}/bin/calcurse";
+    calendar = "${pkgs.calcurse}/bin/calcurse";
+  };
+
+  # Default modules for all users (machines can override with mkForce false)
+  modules.user = {
+    bash.enable = lib.mkDefault true;
+    git.enable = lib.mkDefault true;
+    neovim.enable = lib.mkDefault true;
+    security.gpg.enable = lib.mkDefault true;
+  };
+}