This has been bothering me for a while, so I decided to give it a try: class files generated by the Scala compiler show up in the Open Resource (Ctrl+Shift+R) dialog, which is quite annoying. Unfortunately, it is not possible to exclude certain filename patterns in the UI, instead the corresponding resource needs to be marked derived. I've no idea where the best place to do this is, but I've attached a patch for the EclipseRefinedBuildManager that shows how it could be done.
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