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/gui/default.nix

@@ -0,0 +1,30 @@
+{ lib, config, ... }:
+
+let
+  programs = config.programs;
+
+  defaultBrowser =
+    if programs.firefox.enable then "firefox.desktop"
+    else if programs.brave.enable then "brave-browser.desktop"
+    else if programs.chromium.enable then "chromium.desktop"
+    else null;
+
+  types = [
+    "text/html" "application/xhtml+xml"
+    "x-scheme-handler/http" "x-scheme-handler/https"
+    "application/pdf"
+    "image/png" "image/jpeg" "image/jpg" "image/gif"
+    "image/webp" "image/avif" "image/bmp" "image/tiff" "image/svg+xml"
+    "video/mp4" "video/webm" "video/mkv" "video/avi"
+    "video/x-matroska" "video/quicktime"
+  ];
+
+in
+{
+  xdg.mimeApps = lib.mkIf (defaultBrowser != null) {
+    enable = true;
+    defaultApplications = builtins.listToAttrs (
+      map (t: { name = t; value = [ defaultBrowser ]; }) types
+    );
+  };
+}