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/desktop/hardware.nix

@@ -1,83 +0,0 @@
-{ config, lib, pkgs, modulesPath, ... }:
-
-with lib;
-{
-  imports = [ (modulesPath + "/installer/scan/not-detected.nix") ];
-
-  options.monitors = mkOption {
-    type = types.listOf (types.submodule {
-      options = {
-        name = mkOption { type = types.str; example = "HDMI-A-1"; };
-        width = mkOption { type = types.int; };
-        height = mkOption { type = types.int; };
-        x = mkOption { type = types.int; };
-        y = mkOption { type = types.int; };
-        scale = mkOption { type = types.float; };
-        refreshRate = mkOption { type = types.int; };
-      };
-    });
-    default = [];
-    description = "System monitor configuration";
-  };
-
-  config = {
-    monitors = [
-      { name = "HDMI-A-1"; width = 1920; height = 1080; x = 0;    y = 0; scale = 1.0; refreshRate = 60; }
-      { name = "DP-1";     width = 1920; height = 1080; x = 1920; y = 0; scale = 1.0; refreshRate = 60; }
-    ];
-
-    boot = {
-      initrd = {
-        availableKernelModules = [ "vmd" "xhci_pci" "ahci" "nvme" "usbhid" "usb_storage" "sd_mod" ];
-        kernelModules = [ "dm-snapshot" ];
-      };
-      extraModulePackages = [ ];
-      kernelPackages = pkgs.linuxPackages_zen;
-      kernelParams = [ "intel_iommu=on" ];
-      kernelModules = [ "kvm-intel" "virtio" "vfio-pci" "coretemp" ];
-    };
-
-    environment.systemPackages = with pkgs; [
-      linuxHeaders
-
-      vulkan-headers
-      vulkan-loader
-      vulkan-tools
-      vulkan-extension-layer
-
-      mesa
-      mesa-demos
-
-      cudaPackages.cudatoolkit
-      cudaPackages.cudnn
-    ];
-
-    hardware = {
-      cpu = {
-        intel = {
-          updateMicrocode = lib.mkDefault config.hardware.enableRedistributableFirmware;
-        };
-      };
-      nvidia = {
-        open = true;
-        modesetting.enable = true;
-        nvidiaSettings = true;
-        package = config.boot.kernelPackages.nvidiaPackages.stable;
-      };
-      graphics = {
-        enable = true;
-        enable32Bit = true;
-      };
-    };
-
-    virtualisation.libvirtd = {
-      enable = true;
-      qemu = {
-        runAsRoot = true;
-      };
-    };
-
-    nixpkgs.hostPlatform = lib.mkDefault "x86_64-linux";
-    powerManagement.cpuFreqGovernor = lib.mkDefault "performance";
-  };
-}