Having configuration.nix generation hidden underneath nixos-option never made sense, also given that there was another command to generate part of the configuration (nixos-hardware-scan). Now nixos-generate-config produces both configuration.nix and hardware-configuration.nix. The latter is overwritten while the former is not.
*** NixOS *** NixOS is a Linux distribution based on the purely functional package management system Nix. More information can be found at http://nixos.org/nixos and in the manual in doc/manual.