This is the same for all FreeFlarum forums, and they're beta.15.
It was changed in this commit: flarum/flarum542331b
The commit just split the config in a new file, site.php and then it gets loaded in index.php. No big deal for me, all of our forums work fine without the new version of config.php so you shouldn't worry about it
But this means that files under ./public are ignored during update? In that case, that could be a problem. Just though I'd mention that it happened on FF too, so you're not the only one
Perhaps it happens because we have setup Composer to update flarum/core, but public files are in flarum/flarum?
I guess that you could create both files manually based on the commit too