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

system/machines/wsl/default.nix

@@ -0,0 +1,13 @@
+{ inputs, ... }:
+
+{
+  imports = [
+    inputs.nixos-wsl.nixosModules.wsl
+      (import ./modules/wsl)
+    inputs.home-manager.nixosModules.home-manager
+      (import ./modules/home-manager)
+    ../../../user
+    ../../keys
+    ./system.nix
+  ];
+}

system/machines/wsl/modules/home-manager/default.nix

@@ -0,0 +1,5 @@
+{
+  imports = [
+    ./home.nix
+  ];
+}

system/machines/wsl/modules/home-manager/home.nix

@@ -0,0 +1,24 @@
+{ config, ... }:
+
+{
+  home-manager.useGlobalPkgs = true;
+  home-manager.useUserPackages = true;
+  home-manager.users.${config.user.name} = {
+    imports = [
+      ../../../../../user
+      ../../../../../user/home.nix
+      ../../../../../user/modules
+    ];
+
+    home.stateVersion = "23.11";
+
+    # Machine-specific modules
+    modules.user = {
+      utils = {
+        dev.enable = true;
+        email.enable = true;
+        irc.enable = true;
+      };
+    };
+  };
+}

system/machines/wsl/modules/wsl/default.nix

@@ -0,0 +1,5 @@
+{
+  imports = [
+    ./wsl.nix
+  ];
+}

system/machines/wsl/modules/wsl/wsl.nix

@@ -0,0 +1,20 @@
+{ config, lib, ... }:
+
+{
+  imports = [ ../../../../../user ];
+
+  wsl = rec {
+    enable = true;
+    defaultUser = lib.mkDefault config.user.name;
+    useWindowsDriver = true;
+
+    wslConf = {
+      user.default = lib.mkDefault defaultUser;
+      boot.command = "cd";
+      network = {
+        hostname = "${config.networking.hostName}";
+        generateHosts = true;
+      };
+    };
+  };
+}

system/machines/wsl/system.nix

@@ -0,0 +1,75 @@
+{ pkgs, lib, config, ... }:
+
+{
+  system.stateVersion = "23.11";
+  boot.isContainer = true;
+
+  users.users = {
+    ${config.user.name} = {
+      isNormalUser = true;
+      extraGroups = config.user.groups;
+      openssh.authorizedKeys.keys = [ 
+        "${config.user.keys.ssh.yubikey}" 
+      ];
+    };
+  };
+
+  nix = {
+    channel.enable = false;
+    package = pkgs.nixVersions.stable;
+    extraOptions = ''
+      experimental-features = nix-command flakes
+    '';
+    settings = {
+      auto-optimise-store = true;
+      trusted-users = [ "${config.user.name}" ];
+    };
+    gc = {
+      automatic = true;
+      dates = "daily";
+      options = "--delete-older-than 7d";
+    };
+  };
+
+  security.sudo = {
+    wheelNeedsPassword = false;
+    execWheelOnly = true;
+  };
+
+  time = {
+    timeZone = "America/New_York";
+  };
+
+  i18n.defaultLocale = "en_US.UTF-8";
+
+  console = {
+    font = "Lat2-Terminus16";
+    useXkbConfig = true;
+  };
+
+  networking = {
+    hostName = "wsl";
+    useDHCP = lib.mkDefault true;
+    firewall = {
+      enable = true;
+      allowedTCPPorts = [ 22 80 443 ];
+    };
+  };
+
+  services = {
+    openssh = {
+      enable = true;
+      startWhenNeeded = true;
+      settings = {
+        X11Forwarding = false;
+        PasswordAuthentication = false;
+      };
+    };
+    timesyncd = lib.mkDefault {
+      enable = true;
+      servers = [
+        "time.windows.com"
+      ];
+    };
+  };
+}