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/gui/wm/sway/default.nix

@@ -1,177 +0,0 @@
-{ pkgs, lib, config, monitors ? [], ... }:
-
-with lib;
-let
-  cfg = config.modules.user.gui.wm.sway;
-  modifier = config.wayland.windowManager.sway.config.modifier;
-
-  wallpaper = builtins.fetchurl {
-    url = "https://images6.alphacoders.com/117/1174033.png";
-    sha256 = "1ph5m9s57076jx6042iipqx2ifzadmd5z4lf5l49wgq4jb92mp16";
-  };
-
-  barStatus = pkgs.writeShellScript "status.sh" ''
-    #!/usr/bin/env bash
-    while :; do
-      echo "$(ip -4 addr show eno1 | awk '/inet / {print $2}' | cut -d'/' -f1) | $(free -h | awk '/^Mem/ {print $3}') | $(date +'%I:%M:%S %p') | $(date +'%m-%d-%Y')"; sleep 1;
-    done
-  '';
-
-  toSwayOutput = m: {
-    "${m.name}" = {
-      resolution = "${toString m.width}x${toString m.height}@${toString m.refreshRate}Hz";
-      position = "${toString m.x} ${toString m.y}";
-      scale = toString m.scale;
-      bg = "${wallpaper} fill";
-    };
-  };
-
-  outputConfig = if monitors != []
-    then lib.mkMerge (map toSwayOutput monitors)
-    else {
-      "*" = { bg = "${wallpaper} fill"; };
-    };
-
-in
-{ options.modules.user.gui.wm.sway = { enable = mkEnableOption "Enable Sway WM"; };
-  config = mkIf cfg.enable {
-    wayland.windowManager.sway = {
-      enable = true;
-      xwayland = true;
-      wrapperFeatures.gtk = true;
-
-      extraSessionCommands = ''
-        export _JAVA_AWT_WM_NONREPARENTING=1
-        export GTK_THEME=Adwaita-Dark
-      '';
-
-      config = {
-        defaultWorkspace = "workspace number 1";
-
-        fonts = {
-          names = [ "Terminus" ];
-        };
-
-        output = outputConfig;
-        modifier = "Mod1";
-        menu = "rofi -show drun -show-icons -drun-icon-theme Qogir -font 'Noto Sans 14'";
-        terminal = "${pkgs.alacritty}/bin/alacritty";
-
-        input = {
-          keyboard = {
-            xkb_numlock = "enabled";
-            xkb_layout = "us";
-          };
-          pointer = {
-            accel_profile = "flat";
-            pointer_accel = "0.65";
-          };
-        };
-
-        bars = [
-          {
-            position = "top";
-            statusCommand = "${barStatus}";
-            fonts = {
-              names = [ "Terminus" ];
-              size = 12.0;
-            };
-            colors = {
-              background = "#0A0E14";
-              statusline = "#FFFFFF";
-            };
-          }
-        ];
-
-        gaps = {
-          smartGaps = false;
-          inner = 10;
-        };
-
-        floating = {
-          titlebar = false;
-          border = 0;
-          criteria = [
-            {
-              title = "Android Emulator";
-            }
-          ];
-        };
-
-        window = {
-          titlebar = false;
-          border= 0;
-        };
-
-        keybindings = lib.mkOptionDefault {
-          "${modifier}+q" = "kill";
-          "Print" = "exec grim ~/Pictures/screenshot-$(date +'%Y%m%d-%H%M%S').png";
-          "${modifier}+Shift+Print" = "exec grim -g \"$(slurp)\" ~/Pictures/screenshot-$(date +'%Y%m%d-%H%M%S').png";
-          "${modifier}+Print" = ''exec sh -c 'grim -g "$(swaymsg -t get_tree | jq -j '"'"'.. | select(.type?) | select(.focused).rect | "\(.x),\(.y) \(.width)x\(.height)"'"'"')" ~/Pictures/screenshot-$(date +'%Y%m%d-%H%M%S').png' '';
-          "${modifier}+Shift+f" = "exec alacritty -e sh -c 'EDITOR=nvim ranger'";
-          "${modifier}+Shift+d" = "exec rofi -modi emoji -show emoji";
-        };
-      };
-
-      extraConfig = ''
-        exec_always ${pkgs.autotiling}/bin/autotiling -sr "1.61"
-      '';
-    };
-
-    programs.rofi = import ./config/rofi { inherit pkgs config lib; };
-
-    home.file.".config/rofi" = {
-      source = ./config/rofi/config;
-      recursive = true;
-    };
-    
-    xdg = {
-      portal = {
-        enable = true;
-        extraPortals = with pkgs; [
-          xdg-desktop-portal-wlr
-        ];
-        config.common.default = "*";
-      };
-    };
-
-    #gtk = {
-    #  enable = true;
-    #  theme.package = pkgs.juno-theme;
-    #  theme.name = "Juno-ocean";
-    #  iconTheme.package = pkgs.qogir-icon-theme;
-    #  iconTheme.name = "Qogir";
-    #};
-
-    qt = {
-      enable = true;
-      style.package = pkgs.juno-theme;
-      platformTheme.name = "gtk";
-    };
-
-    home.packages = with pkgs; [
-      pavucontrol
-      xdg-utils
-      wl-clipboard
-      autotiling
-
-      grim
-      jq
-      slurp
-
-      ranger
-      highlight
-
-      nerd-fonts.terminess-ttf
-      noto-fonts
-      noto-fonts-cjk-sans
-      noto-fonts-color-emoji
-    ];
-
-    programs = {
-      imv.enable = true;
-    };
-
-    fonts.fontconfig.enable = true;
-  };
-}