ERROR: ERROR ITMS-90047: "Disallowed paths ( "iTunesMetadata.plist" ) found at: MyNewTool.app"

Solution:

For command line or IDE builds with XamarinVS

1. Ensure "Project Properties -> iOS IPA Options -> Include Artwork in IPA" is not checked. (Or manually set the BuildIpa and IpaIncludeArtwork properties as mentioned above.)
   
2. Build the app.
3. Submit the .ipa file using Application Loader.

or

<Target Name="_CompileITunesMetadata" DependsOnTargets="_DetectSdkLocations;_DetectAppManifest;_GenerateBundleName;_CompileAppManifest">
  <Message Text="Skipping CompileITunesMetadata task to prevent inclusion of iTunesMetadata.plist in the IPA" />
</Target>

Source:

1. https://forums.xamarin.com/discussion/40388/disallowed-paths-itunesmetadata-plist-found-at-when-submitting-to-app-store/p1
2. https://discussions.apple.com/thread/6997898?start=0&tstart=0
3. https://bugzilla.xamarin.com/show_bug.cgi?id=29180#c0