Finally found this answer: http://stackoverflow.com/questions/23229864/how-can-i-show-a-source-directory-to-sbteclipse-without-adding-it-to-the-compile to a question: how to include integration test sources in Scala IDE (Eclipse) - just add the following line to your build.sbt:
EclipseKeys.configurations := Set(Compile, Test, IntegrationTest)