This question appears fundamentally the same as Linker error in ScalaJS: "Referring to non-existent class", but seems to differ in specifics. I don't specify a JVM version in build.sbt.
I'm trying to access a file in my scalajs app using scala.io.Source, or java.io.File. As soon as I attempt to use either I get a link fail:
[info] Fast optimizing C:\Users\Tim\Documents\GitHub\binpack\target\scala-2.11\binpack-fastopt.js
[error] Referring to non-existent class java.io.File
[error] called from client.jsClient$.onFileChosen(japgolly.scalajs.react.SyntheticEvent)scala.Function0
java.io.File is not portable to Scala.js because it's specifically tied to the JVM. See http://www.lihaoyi.com/hands-on-scala-js/#PortingJavaAPIs (just scroll to the very bottom) for a little more detail.