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/wm/hyprland/config/waybar/style.css

@@ -0,0 +1,73 @@
+* {
+  border: none;
+  font-size: 14px;
+  font-family: "Terminus Nerd Font Propo" ;
+  min-height: 25px;
+}
+
+window#waybar {
+  background: transparent;
+  margin: 5px;
+ }
+
+#custom-logo {
+  padding: 0 10px;
+  color: #5277c3;
+}
+
+.modules-right {
+  padding-left: 5px;
+  border-radius: 15px 0 0 15px;
+  margin-top: 2px;
+  background: #000000;
+}
+
+.modules-center {
+  padding: 0 15px;
+  margin-top: 2px;
+  border-radius: 15px 15px 15px 15px;
+  background: #000000;
+}
+
+.modules-left {
+  border-radius: 0 15px 15px 0;
+  margin-top: 2px;
+  background: #000000;
+}
+
+#custom-clipboard,
+#pulseaudio,
+#network,
+#disk,
+#memory,
+#backlight,
+#cpu,
+#temperature,
+#custom-weather,
+#jack,
+#tray,
+#window,
+#workspaces,
+#clock {
+  padding: 0 5px;
+}
+#pulseaudio {
+  padding-top: 3px;
+}
+
+#temperature.critical,
+#pulseaudio.muted {
+  color: #FF0000;
+  padding-top: 0;
+}
+
+#clock{
+  color: #5fd1fa;
+}
+
+@keyframes blink {
+  to {
+    background-color: #ffffff;
+    color: #000000;
+  }
+}