This change https://gerrit.wikimedia.org/r/#/c/166705/16/includes/GlobalFunctions.php introduced the assumption that your exensions and skins folders are subfolders of your installation path. We already have $wgExtensionAssetsPath and $wgStyleDirectory (badly named!) which allow you to override this assumption.
- use $wgStyleDirectory anywhere $IP/skins was introduced
- create a $wgExtensionDirectory and replace $IP/extensions with it