I was hoping to improve the documentation of pijul clone a bit, but it seems like the file that is references (and that appears in the rendered mdbook) is entirely absent?

My understanding is that documentation is generated from the help output of the pijul binary, so you probably want to change the source code of the binary itself. The current setup uses clap_derive and the relevant file can be found here (the Clone struct on line 10 would be a good place to start). If you have any problems, the Zulip chat is quite active :)