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

system/machines/desktop/README.md

@@ -0,0 +1,19 @@
+## Hardware
+
+| Component   | Model                              |
+|-------------|------------------------------------|
+| Motherboard | MSI B760 GAMING PLUS WIFI          |
+| CPU         | Intel Core i7-12700KF (12th Gen)   |
+| GPU         | NVIDIA GeForce GTX 1650            |
+| Storage     | 2x 2TB Crucial MX500 SSD           |
+
+## Memory
+
+| Slot    | Size | Manufacturer   | Part Number | Speed      |
+|---------|------|----------------|-------------|------------|
+| DIMM A1 | -    | -              | -           | -          |
+| DIMM A2 | 16GB | Team Group Inc | UD5-6000    | 4800 MT/s  |
+| DIMM B1 | -    | -              | -           | -          |
+| DIMM B2 | 16GB | Team Group Inc | UD5-6000    | 4800 MT/s  |
+
+**Total: 32GB DDR5**