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Using this test project: https://github.com/baulig/upgraded-adventure
It's a Xamarin.Mac app, which references a Xamarin.Mac library. The library defines a storyboard, a main window and main menu.
When using xbuild, the relevant resources are added to the .app directory. This does not happen with msbuild.
See the https://github.com/baulig/upgraded-adventure/blob/master/filelist-msbuild.txt and
I worked around the problem by explicitly source-linking all the files in my app instead of using a library.
This has been fixed (duplicate of another bug, too lazy to find it right now)