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

.gitmodules

@@ -1,15 +1,15 @@
 [submodule "nvim"]
-	path = src/user/modules/utils/modules/neovim/config/nvim
+	path = user/modules/neovim/nvim
 	url = https://github.com/itme-brain/nvim.git
 
 [submodule "vim"]
-	path = src/user/modules/utils/modules/vim/vim
+	path = user/modules/vim/vim
 	url = https://github.com/itme-brain/vim.git
 
 [submodule "git"]
-	path = src/user/modules/git/git
+	path = user/modules/git/git
 	url = https://github.com/itme-brain/git.git
 
 [submodule "bash"]
-	path = src/user/modules/bash/config/bash
+	path = user/modules/bash/bash
 	url = https://github.com/itme-brain/bash.git