I think I prefer to keep the user documentation on the website since it makes contributions easier. It is also possible to keep it on this repo and include it in the website like done for this page for example: https://duniter.org/wiki/duniter-v2/configure-docker/.
Also the documentation currently mixes protocol and practical details. I consider that polkadotjs is an advanced tool and that gcli is the way to go. So I would have two pages:
how to become smith (protocol and license)
becoming smith with gcli (examples of command lines)
becoming smith with polkadotjs (more advanced alternative way)
And the protocol part could be explained in more general public readable terms on the website and in more technical terms directly in the pallet readme.