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/server/hardware.nix

@@ -1,30 +0,0 @@
-{ config, lib, pkgs, modulesPath, ... }:
-
-{
-  imports = [
-    (modulesPath + "/installer/scan/not-detected.nix")
-    ./modules/disko
-  ];
-
-  boot = {
-    initrd = {
-      availableKernelModules = [ "xhci_pci" "ehci_pci" "ahci" "usbhid" "sd_mod" "sr_mod" ];
-      kernelModules = [ ];
-    };
-    kernelModules = [ "kvm-intel" ];
-    extraModulePackages = [ ];
-  };
-
-  hardware.cpu.intel.updateMicrocode = lib.mkDefault config.hardware.enableRedistributableFirmware;
-
-  # Enable VAAPI for hardware video acceleration
-  hardware.graphics = {
-    enable = true;
-    extraPackages = with pkgs; [
-      intel-vaapi-driver  # i965 driver for Haswell
-    ];
-  };
-
-  nixpkgs.hostPlatform = lib.mkDefault "x86_64-linux";
-  powerManagement.cpuFreqGovernor = lib.mkDefault "ondemand";
-}