Change default directory for generated sources

[JanBessai]

The src_managed folder should by default adhere to the main/language/package convention. Generated sources are Java code, so they should end up in src_managed/java/package. This especially fixes source duplication bugs in IntelliJ.

[benmccann]

The recommendation is now against using (sourceManaged in Compile).value altogether. Instead each plugin should roll out their own directory under target, and append to managedSourceDirectories in Compile. See https://github.com/sbt/sbt/issues/1664#issuecomment-213057686