Hi Matt,
The documentation here... https://docs.sel4.systems/projects/buildsystem/incorporating.html refers to a build setup that AFAICT is different to the reference application, which I think is here... https://github.com/seL4proj/sel4webserver
The build setup of the reference webserver application is the same as the "kernel directory" setup in the documentation.
It looks a little different as the reference application is just one component of the entire reference system.
If you scroll down a little in the webserver GitHub link, the repo init and repo sync commands pulls the required components of the webserver reference system and organises the components into a directory structure that's similar to the one listed in the "kernel directory" setup in the documentation. The contents of the sel4webserver repository can then be found in the 'projects/webserver' directory after the repo sync command.
Regards, Damon