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

flake.lock

@@ -102,11 +102,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1772822230,
-        "narHash": "sha256-yf3iYLGbGVlIthlQIk5/4/EQDZNNEmuqKZkQssMljuw=",
+        "lastModified": 1773375660,
+        "narHash": "sha256-SEzUWw2Rf5Ki3bcM26nSKgbeoqi2uYy8IHVBqOKjX3w=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "71caefce12ba78d84fe618cf61644dce01cf3a96",
+        "rev": "3e20095fe3c6cbb1ddcef89b26969a69a1570776",
         "type": "github"
       },
       "original": {