target.jvmWithJava isn’t supported actually and going to be removed in the future.
Also, please use the latest available Kotlin 1.3.* version (which is currently 1.3.0-rc-190) — as the topic name says, the new model is introduced in Kotlin 1.3. There is a bug at the documentation site, though, which recommends 1.2.71 version, but it’s going to be fixed soon.
As to JS configuration, please make sure it is configured properly since it indeed requires some additional set up for the proper files generation (which is general for JS part and not specific for the multiplatform, though). To get the idea, have a look at this and this examples.