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/default.nix

@@ -1,39 +0,0 @@
-let
-  mkModules = dir: isRoot:
-    let
-      entries = builtins.readDir dir;
-      names = builtins.attrNames entries;
-      
-      excludedDirs = [ "config" "scripts" ];
-      isSubmodule = path:
-        builtins.pathExists "${path}/.git" &&
-        builtins.readFileType "${path}/.git" == "regular";
-      isModuleDir = path:
-        builtins.pathExists path &&
-        builtins.readFileType path == "directory" &&
-        !(builtins.elem (builtins.baseNameOf path) excludedDirs) &&
-        !(isSubmodule path);
-      isModule = file: file == "default.nix";
-      isNix = file: builtins.match ".*\\.nix" file != null && file != "default.nix";
-
-    in
-      builtins.concatMap (name:
-        let
-          path = "${dir}/${name}";
-        in
-          if isModuleDir path then
-            mkModules path false
-          else if isModule name && !isRoot then
-            [ dir ]
-          else if isNix name then
-            [ path ]
-          else
-            []
-      ) names;
-
-in
-{
-  imports = [
-    ./config
-  ] ++ mkModules ./. true;
-}