Thanks for explaining that, makes more sense to me what you’re doing now!
Pages will always only take into account a root-level
_config.yml file. This means that any config files inside your submodule repositories will be ignored when they are imported, meaning that any specific themes you’ve chosen will be ignored.
If you’re switching to MKDocs then that should solve your problem just fine for this issue, but you may have to make certain considerations if you’re planning to use Jekyll again in future. For example, any Jekyll configuration will need to be made in the
WebThingsIO/webthings.io repository, regardless if you’re using Jekyll for that direct site or not, as the root of that repository is the only place where Pages will look for a config file.
Another alternative would be to host separate Pages sites out of each of your repositories.
I notice that you’re using the
webthings.io custom domain for this site. To keep your existing URLs the same you’ll need to rename your repository from
WebThingsIO/webthingsio.github.io. Doing this will allow this custom domain to be inherited by all other Pages sites listed under your account instead of being hosted from a
Once you’ve made that change you should then be able to go to any other repositories hosted under your GitHub account an enable Pages in their repository settings. Any repositories you do this with will be available at https://webthings.io/repository-name/. If you do this with your
WebThingsIO/docs repository your site will then be hosted on Pages, with the correct Jekyll theme, at https://webthings.io/docs/.
If you’re unhappy changing the name of your
WebThingsIO/webthings.io repository then you can still do this, though any existing domains will no longer work and Pages sites outside of this repository will be hosted from a
github.io address (unless you add a different custom domain/subdomain to them in the repository settings).
You can choose to mix and match this approach—where some repositories are included as submodules and others are hosted as separate sites—but any Jekyll site will need to be hosted as a separate repository or will need to rely on the config file from the root repository.
[Edited to fix an incorrect repository name]