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/gui/alacritty/config/alacritty.nix

@@ -0,0 +1,83 @@
+{ config, ... }:
+
+let
+hyprland = config.modules.user.gui.wm.hyprland;
+
+in
+{
+  scrolling = {
+    history = 10000;
+    multiplier = 3;
+  };
+
+  window = {
+    opacity = if hyprland.enable then 0.9 else 1;
+  };
+
+  keyboard.bindings = [
+    {
+      key = "Enter";
+      mods = "Alt | Shift";
+      action = "SpawnNewInstance";
+    }
+  ];
+
+  colors = {
+    primary = {
+      background = "#000000";
+      foreground = "#cdd6f4";
+    };
+
+    normal = {
+      black   = "#1e2127";
+      red     = "#e06c75";
+      green   = "#98c379";
+      yellow  = "#d19a66";
+      blue    = "#61afef";
+      magenta = "#c678dd";
+      cyan    = "#56b6c2";
+      white   = "#abb2bf";
+    };
+
+    bright = {
+      black   =  "#5c6370";
+      red     =  "#e06c75";
+      green   =  "#98c379";
+      yellow  =  "#d19a66";
+      blue    =  "#61afef";
+      magenta =  "#c678dd";
+      cyan    =  "#56b6c2";
+      white   =  "#ffffff";
+    };
+  };
+
+  font = {
+    size = 12;
+    normal = {
+      family = "Terminess Nerd Font Propo";
+      style = "Regular";
+    };
+
+    bold = {
+      family = "Terminess Nerd Font Propo";
+      style = "Bold";
+    };
+
+    italic = {
+      family = "Terminess Nerd Font Propo";
+      style = "Italic";
+    };
+
+    bold_italic = {
+      family = "Terminess Nerd Font Propo";
+      style = "Bold Italic";
+    };
+  };
+
+
+  #cursor = {
+  #  shape = "Block";
+  #  blinking = "Always";
+  #  blink_interval = 750;
+  #};
+}

user/modules/gui/alacritty/default.nix

@@ -0,0 +1,15 @@
+{ lib, config, ... }:
+
+with lib;
+let
+  cfg = config.modules.user.gui.alacritty;
+
+in
+{ options.modules.user.gui.alacritty = { enable = mkEnableOption "Enable Alacritty terminal"; };
+  config = mkIf cfg.enable {
+    programs.alacritty = {
+      enable = true;
+      settings = import ./config/alacritty.nix { inherit config; };
+    };
+  };
+}