Missing Provisioning Profile :Apps must contain a provisioning profile in a file named embedded.mobileprovision

I tried to clear out the provisioning profiles and none of it did help. What changed from the previous XCode version to this one is the build system. By changing your build system back to the legacy one, this was resolved for me.

You can switch out the build system under file > workspace settings (or project settings) and then select Legacy Build System under Build System (see screenshot).

Good luck!

Edit: As of cordovo iOS 5.0.0 the new build system is now supported. Changelog can be found over here: https://cordova.apache.org/announcements/2019/02/09/cordova-ios-release-5.0.0.html