How can I fix missing conf files when using shadowJar and Scala dependencies?

The resulting fix was to add the following to the build.gradle file:

shadowJar {
  transform(com.github.jengelman.gradle.plugins.shadow.transformers.AppendingTransformer) {
    resource = 'reference.conf'
  }
}

Solution was found here:http://www.sureshpw.com/2015/10/building-akka-bundle-with-all.html

Simply:

  shadowJar {
    append('reference.conf')
  }

See Controlling JAR Content Merging