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/modules/utils/dev/default.nix

@@ -0,0 +1,56 @@
+{ pkgs, lib, config, osConfig, ... }:
+
+with lib;
+let
+  cfg = config.modules.user.utils.dev;
+
+in
+{ options.modules.user.utils.dev = { enable = mkEnableOption "user.utils.dev"; };
+  config = mkIf cfg.enable {
+    home.packages = with pkgs; [
+      claude-code
+
+      nix-init
+      nix-prefetch-git
+      nurl
+
+      pkg-config
+      qrencode
+
+      docker
+
+      # Network/system tools
+      fping
+      wireguard-tools
+      pciutils
+      lshw
+    ] ++ optionals (osConfig.virtualisation.libvirtd.enable) [
+      virt-manager
+    ];
+
+    programs = {
+      #bash = {
+      #  initExtra = import ./config/penpot.nix;
+      #};
+      direnv = {
+        enable = true;
+        enableBashIntegration = true;
+        nix-direnv.enable = true;
+      };
+    };
+
+    home = {
+      sessionVariables = {
+        DIRENV_LOG_FORMAT = "";
+      };
+
+      # Workaround for direnv_log bug 
+      # https://github.com/direnv/direnv/issues/1418#issuecomment-2820125413
+      file.".config/direnv/direnv.toml" = {
+        enable = true;
+        force = true;
+        text = "";
+      };
+    };
+  };
+}