Add to your project/plugin.sbt:
addSbtPlugin("com.typesafe.sbt" % "sbt-start-script" % "0.10.0")
addSbtPlugin("org.scala-sbt.plugins" % "sbt-onejar" % "0.8")
Update:
Activator has own file "activator-sbt-eclipse-shim.sbt" It contains:
addSbtPlugin("com.typesafe.sbteclipse" % "sbteclipse-plugin" % "2.3.0")
Remove "com.typesafe.sbteclipse" % "sbteclipse-plugin" from plugin.sbt.
I changed it to 2.4.0 - and the problem was solved. But after restart activator it again restore 2.3.0 - but the error did not occur any more.
Then I generated project for eclipse/idea. Both finished with success.