The cause was the publishing source. Pages was configured to build the gh-pages branch from the /docs subdirectory, but the site itself — _config.yml, index.md, the stylesheet — sat at the branch root, one level above what Pages was serving. The only file inside /docs was a stub page at docs/wrifo/index.md. That page worked fine at /wrifo/; nothing else existed as far as the server was concerned. Without a _config.yml in the publishing root, Jekyll was not applying a theme either.

What changed

The site is now built by a GitHub Actions workflow rather than by the legacy Pages builder, and everything lives on main — the gh-pages branch is gone. That combination removes the class of bug entirely: with a workflow build there is no “publishing source” setting to get out of step with the repository, because the branch that gets published is the one named in the workflow file.

The site also has a CNAME file tracked in git rather than relying only on the repository setting. Changing the Pages source through the API silently clears the custom domain, so it is worth having in a file that gets republished every build.

The stock remote theme is gone. Layouts, includes, and the stylesheet are all in the repository now, which makes the site slower to change casually and easier to change deliberately.

Contributing

The site is plain Jekyll. To preview changes locally:

bundle install
bundle exec jekyll serve

Posts go in _posts as YYYY-MM-DD-slug.md. Pages go at the top level with a permalink in their front matter. Sections listed in the nav key of _config.yml show up both in the header and as tips on the branching hypha on the home page. Pushing to main publishes.