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

src/system/machines/wsl/system.nix

@@ -1,75 +0,0 @@
-{ 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"
-      ];
-    };
-  };
-}