Great! That’s a quite extensive example covering many of the multiplatform language features. We probably could use it as a test site.
Note that the multiplatform tooling is being actively developed, so you might get more smooth experience with the recent fixes published in eap builds of the plugin, or even in the latest development build of the plugin. The corresponding gradle plugin and the standard library for the latter build are published to this bintray repository: JFrog Distribution: Get your software to where it needs to be -- ASAP!
Could you create a branch where that fails and report it to our issue tracker?
Probably you should delegate IDE build/run actions to gradle for your project. There is corresponding setting in Build Tools → Gradle → Runner group in settings.
That the feature is unreleased and unfinished shows, but I have converted one of my libraries and are satisfied with the possibilities and stability. I am using the stable releases of Kotlin (1.1.3-2), and I have not encountered issues with a successfully built JAR at run time yet. Here you can see which capabilities I used: https://github.com/squins/ooverkommelig/tree/multi-platform