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