I've just checked through the Notification Center changes and there's still no way of waking the main app or communicating to it while it's in the background that I can find. WatchKit gave us +openParentApplication:, which is really useful. Given that they're both extensions, why hasn't the same functionality made its way to Notification Center widgets?
Still no +openParentApplication: equivalent for Today view extensions
The weird part is that - (BOOL)application:(UIApplication *)application openURL:(NSURL *)url sourceApplication:(NSString *)sourceApplication annotation:(id)annotation is deprecated on iOS 9 but Apple would want us to continue to support it so the Today Extension can open the containing app?