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

systems/common.nix

@@ -16,7 +16,7 @@
         networkmanager-openconnect
       ];
     };
-    useDHCP = false; # Depreciated
+    useDHCP = false; # Deprecated
   };
 
   # Bootloader
@@ -47,7 +47,6 @@
   nixpkgs.config.allowUnfree = true;
   nixpkgs.config.nvidia.acceptLicense = true;
   nixpkgs.config.nvidia.libsOnly = true;
-  nixpkgs.config.allowBroken = true;
 
   # Location & internationalisation
   time.timeZone = "America/Los_Angeles";
@@ -73,12 +72,10 @@
     pulse.enable = true;
   };
   services.openssh.enable = true;
-  # Temporarily disabled to avoid build cycle errors
-  # programs.java.enable = true; 
   security.polkit.enable = true;
   programs.zsh.enable = true;
   security.sudo.wheelNeedsPassword = false;
-  
+
   # System packages
   environment.systemPackages = with pkgs; [
     fzf
@@ -137,7 +134,7 @@
   ];
 
   services.xserver.excludePackages = [ pkgs.xterm ];
-  documentation.nixos.enable = false; 
+  documentation.nixos.enable = false;
 
   systemd.network.wait-online.enable = false;
   boot.initrd.systemd.network.wait-online.enable = false;