Some configuration settings are path based:
$wgTorOnionooCA = __DIR__ . "/torproject.crt";
or
$GLOBALS['wgBabelLanguageCodesCdb'] = __DIR__ . '/codes.cdb'; $GLOBALS['wgBabelLanguageNamesCdb'] = __DIR__ . '/names.cdb';
We should be able to indicate that these settings are path based, and set them appropriately.