chore: Clean up repository code and structure

- Removed commented packages: cura, parsec-bin, bottles, stremio, gimp, calibre
- Removed commented code: Java enable, low-latency kernel, ROCm packages, bridges
- Removed trailing whitespace across multiple files
- Fixed typo: Depreciated -> Deprecated in networking
- Removed unused desktop/gnome.nix module (not referenced)
- Removed systems/common-headless.nix (duplicates common.nix)
- Removed nixpkgs.config.allowBroken setting
- Added result, *.swp, *~ to .gitignore
- Removed .clinerules file (deprecated, info in docs/agents.md)
- Updated docs/agents.md changelog with cleanup details

desktop/3dprinting.nix

@@ -3,7 +3,6 @@
 {
 
 environment.systemPackages = with pkgs; [
-#  cura
   freecad
   super-slicer
   openscad

desktop/daw.nix

@@ -29,6 +29,4 @@
     vital       # free version if you want
   ];
 
-  # Optional: low-latency kernel (for extreme cases)
-  # boot.kernelPackages = pkgs.linuxPackages_lowlatency;
 }

desktop/gaming.nix

@@ -4,8 +4,6 @@
 
   environment.systemPackages = with pkgs; [
     discord       # Gaming communication
-#   parsec-bin
-#   bottles
   ];
 
   # Steam

desktop/gnome.nix

@@ -1,114 +0,0 @@
-  { config, pkgs, home-manager, ... }:
-
-  {
-  services.xserver.enable = true;
-  services.xserver.displayManager.gdm.enable = true;
-  services.xserver.desktopManager.gnome.enable = true;
-  services.xserver.displayManager.gdm.wayland   = false;
-  services.xserver = {
-    layout = "us";
-    xkbVariant = "";
-  };
-    # Exclude gnome garbage
-  environment.gnome.excludePackages = (with pkgs; [
-    gnome-photos
-    gnome-tour
-  ]) ++ (with pkgs.gnome; [
-    gnome-weather
-    cheese # webcam tool
-    gnome-music
-    gedit # text editor
-    epiphany # web browser
-    geary # email reader
-    evince # document viewer
-    gnome-characters
-    totem # video player
-    tali # poker game
-    iagno # go game
-    hitori # sudoku game
-    atomix # puzzle game
-    ]
-  );
-home-manager.users.jsutter = {
-  gtk = {
-    enable = true;
-    iconTheme = {
-      name = "Papirus-Dark";
-      package = pkgs.papirus-icon-theme;
-    };
-    theme = {
-      name = "palenight";
-      package = pkgs.palenight-theme;
-    };
-    cursorTheme = {
-      name = "Numix-Cursor";
-      package = pkgs.numix-cursor-theme;
-    };
-    gtk3.extraConfig = {
-      Settings = ''
-        gtk-application-prefer-dark-theme=1
-      '';
-    };
-    gtk4.extraConfig = {
-      Settings = ''
-        gtk-application-prefer-dark-theme=1
-      '';
-    };
-  };
-  dconf.settings = {
-    "org/gnome/mutter" = {
-      experimental-features = [ "scale-monitor-framebuffer" ];
-    };
-    "org/gnome/shell" = {
-      favorite-apps = [
-        "org.gnome.Console.desktop"
-        "firefox.desktop"
-        "slack.desktop"
-        "codium.desktop"
-        "com.nextcloud.desktopclient.nextcloud.desktop"
-        "Zoom.desktop"
-        "steam.desktop"
-        "vmware-view.desktop"
-      ];
-    };
-    "org/gnome/desktop/interface" = {
-      color-scheme = "prefer-dark";
-      enable-hot-corners = false;
-    };
-    "org/gnome/desktop/wm/preferences" = {
-      workspace-names = [ "Main" ];
-    };
-    "org/gnome/desktop/background" = {
-      picture-uri = "https://git.sym.bio/jsutter/backgrounds/-/raw/main/2.jpg";
-      picture-uri-dark = "https://git.sym.bio/jsutter/backgrounds/-/raw/main/3.jpg";
-    };
-    "org/gnome/desktop/screensaver" = {
-      picture-uri = "https://git.sym.bio/jsutter/backgrounds/-/raw/main/4.jpg";
-      primary-color = "#3465a4";
-      secondary-color = "#000000";
-    };
-    "org/gnome/shell" = {
-      disable-user-extensions = false;
-      enabled-extensions = [ # "gnome-extensions list" to get a list.
-        "user-theme@gnome-shell-extensions.gcampax.github.com"
-        "trayIconsReloaded@selfmade.pl"
-        "dash-to-panel@jderose9.github.com"
-      ];
-    };
-  };
-  home.packages = with pkgs; [
-    gnomeExtensions.user-themes
-    gnomeExtensions.tray-icons-reloaded
-    gnomeExtensions.dash-to-panel
-    gnomeExtensions.cpufreq
-  ];
-  home.sessionVariables.GTK_THEME = "palenight";
-  };
-  # GNUPG Stuff 
-  services.pcscd.enable = true;
-  programs.gnupg.agent = {
-    enable = true;
-    pinentryFlavor = "gnome3";
-    enableSSHSupport = true;
-  };
-}

desktop/media.nix

@@ -4,7 +4,6 @@
   environment.systemPackages = with pkgs; [
     vlc           # Media player
     deluge        # BitTorrent client
-#    stremio
   ];
 
 

desktop/office.nix

@@ -8,8 +8,6 @@
     pkgs-unstable.signal-desktop # Private messaging
     freerdp          # xfreerdp CLI client
     remmina          # GTK GUI RDP client
-#   gimp  # Temporarily commented out to avoid build errors
-#   calibre
   ];
 
   #for zoom

desktop/virtualization.nix

@@ -63,5 +63,4 @@ systemd.services.network-debug = {
 
   virtualisation.libvirtd.allowedBridges =
     [ "br0" ];
-    
 }