The phrase "from scratch" was originally a sports analogy meaning from the starting line, like a footrace, or a facing line like in boxing. A line in chalk was scratched into the ground. So in this case it means from the beginning, which even using AI, it is. The boxers come to the ring to fight from scratch, but they've had years of training and watched countless boxing matches to learn. Both the CentOS creator and the AI agent have learned immense amounts of information from a lot of other people's open source work, but they started making a new OS from the beginning or the scratch line.