Kotlin keeps additional package metadata in .kotlin_module files; however, these files are not adjusted automatically when relocate function of shadow plugin is used. This does not prevent proper usage of the resulting libraries at runtime, but can cause issues if you try to compile Kotlin code against libraries with such relocated packages, as Kotlin compiler uses this metadata to filter out packages.

There is a kotlinx-metadata-jvm library that can manipulate (read/write) Kotlin metadata, including .kotlin_module files. I can make a PR to support automatic package relocation in Kotlin metadata when relocate is used. Will you accept this sort of contribution?