Refactor: Simplify module structure and reorganize services

- Removed system/ directory, merged applications into users/geir.nix
- Simplified fonts.nix to bare minimum (users can add more)
- Moved transmission.nix to sleeper-service/services/ (machine-specific)
- Organized grey-area services into services/ directory
- Updated import paths and tested all configurations
- Added research documentation for deploy-rs and GNU Stow

machines/congenital-optimist/configuration.nix

@@ -12,10 +12,6 @@
     # Security modules
     ../../modules/security/ssh-keys.nix
     
-    # System modules
-    ../../modules/system/fonts.nix
-    ../../modules/system/applications.nix
-    
     # Hardware modules
     ../../modules/hardware/amd-workstation.nix