the Name.php entry points will probably start being removed at some point in the future in favor of the extension registration system. Instead of require_once'ing those, jenkins should just call wfLoadExtension(' Name' ); Skins should use wfLoadSkin() instead.
Additionally, we should have a job that runs the validateRegistrationFile.php script if the extension.json or skin.json file is modified. This script depends upon the justinrainbow/json-schema library which is not in mediawiki/vendor since it's just a development dependency.