The generated MediaWiki PHP documentation has an Introduction section. All the sections under this in the left-hand nav (Introduction > Introduction, Setup, File Operations...) come from includes/filebackend/README. The intent in the README markup is they should appear in a separate File Backend section:
/*! \ingroup FileBackend \page file_backend_design File backend design
The same material appears under Modules > File backend in the left nav if you scroll down to File backend design, and there's a link to it when you click More... in the introduction to Modules > File backend. So just discourage the material from appearing in the top-level Introduction as well.