Remove old genetics CLI once #1038 merged

[hmacdope]

@mariacm12 amazing work, thanks so much for doing this, you are an absolute legend. I have made some small changes just removing some CLI args that are repeated but other than that looks perfect. I am happy to have the CLI and args live in genetics, I think that is its natural home.

If you could just confirm that things work I think we should be good to go here. We can remove old CLI in a separate PR.