Upgrade to 4.7 breaks custom php
This does appear to be a legitimate issue, so I've created a bug in the tracker here: https://issues.civicrm.org/jira/browse/CRM-18079

Generally it's better not to use this folder for maintainability reasons - it is better to use an extension - but since it is an advertised piece of functionality, it should work as intended!

Thanks for reporting this.