Additionally to the runtime.fetch setting, you need to double check that any xrefs have the adoc extension specified.
In antora 2, this extension was automatically added if missing. That is no longer the case in 3.0 [1]. For example, in your site.yml, site.start_page should be fedora-server::index.adoc Same for <module>/antora.yml, start_page will became ROOT:index.adoc
[1]: https://docs.antora.org/antora/latest/install/upgrade-antora/#checklist