Currently when doing an Xcode build, you'll get the following error, when trying to submit the app to the App Store:

ERROR ITMS-90339: "This bundle is invalid. The Info.plist contains an invalid key 'CFBundleResourceSpecification' in bundle myApp [myApp.app]"

This is caused by the deprecated CFBundleResourceSpecification / ResourceRules.plist.
It seems that Apple suggests to use xcodebuild instead of PackageApplication now.

When I remove the ResourceList.plist from "Custom xcodebuild arguments", I get the following error:
/var/folders/7q/9zh9m0fx4631vm0y_jdrgmnw00007q/T/ziGbi_t11S/Payload/myApp.app/ResourceRules.plist: cannot read resources

See also:
https://forums.developer.apple.com/thread/19832
http://stackoverflow.com/questions/32763288