When packages get renamed during shading, no changes are made to any the ScalaSignature annotations in those JARs. The result is that Scala reflection will fail silently.

I imagine the fix would be to read and rewrite the ScalaSignature annotations along with the bytecode changes made by JarJar. It it easy enough to decode the signature using scalap and rewrite the annotation using ASM, but I didn't see any way to modify and re-pickle the signature without extracting pieces of scalac.