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/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