Has anyone figured out a way to suppress Maps, iBooks and Photos in El Capitan yet? In previous releases Apple has copied/moved the com.apple.dockfixup.plist, unless it is being done some other way.
I use dockutil to create a custom dock and throw it into the user template before anyone logs in so that everyone at least starts out with the same dock that they can modify as they wish -- but those three apps seem to be added by Apple after the fact via some new mechanism.
