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

user/modules/neovim/pkgs.nix

@@ -0,0 +1,24 @@
+{ pkgs, ... }:
+
+let
+  # Essential LSPs for config files (project-specific LSPs go in devShells)
+  lsp = with pkgs; [
+    nixd
+    lua-language-server
+    marksman
+    taplo
+  ];
+
+  lsp' = with pkgs.nodePackages; [
+    vscode-langservers-extracted  # jsonls, html, cssls
+    bash-language-server
+    yaml-language-server
+  ];
+
+  extraPackages = with pkgs; [
+    lazygit
+    gcc
+  ];
+
+in
+  extraPackages ++ lsp ++ lsp'