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/user/modules/tmux/default.nix

@@ -1,37 +0,0 @@
-{ pkgs, lib, config, ... }:
-
-with lib;
-let
-  cfg = config.modules.user.tmux;
-  gui = config.modules.user.gui.wm;
-
-  wm = {
-    enable = builtins.any (mod: mod.enable or false) (builtins.attrValues gui);
-  };
-
-in
-{ options.modules.user.tmux = { enable = mkEnableOption "Enable tmux module"; };
-  config = mkIf cfg.enable {
-    programs.tmux = {
-      enable = true;
-      newSession = true;
-      disableConfirmationPrompt = true;
-      keyMode = "vi";
-      mouse = if wm.enable then true else false;
-
-      prefix = "M";
-      #shell = "\${pkgs.bash}/bin/bash";
-
-      plugins = with pkgs.tmuxPlugins; [
-        {
-          plugin = tilish;
-          extraConfig = ''
-            set -g @tilish-default 'tiled'
-          '';
-        }
-      ];
-
-      extraConfig = import ./config/tmux.nix;
-    };
-  };
-}