Microsoft's new look for Document Libraries doesn't seem to use my custom master page. This article (http://www.jasperoosterveld.com/2016/06/adopting-the-modern-sharepoint-online-document-libraries/) says custom master pages aren't supported at the moment. That implies it may come later.
Has anyone else had to address this yet? The primary need of the custom master page is load some external javascript files. Changing the "SharePoint Lists and Libraries experience" from new to classic seems to be the best temporary fix.