See sbt/sbt-eclipse#295 and sbt/sbt-pgp#80.

I have installed sbteclipse as a global plugin (since in most of my builds nothing depends on it). I have some configuration for it in ~/.sbt/0.13/sbteclipse.sbt, that uses EclipseKeys unqualified. When I switched from 2.5.0 to 4.0.0, I needed to add an import there for EclipseKeys. This is not needed if I place the setting in build.sbt, whether the plugin is installed locally or globally.

For sbteclipse, it seems that's only needed with versions of the plugin after switching to the 0.13.5 plugin architecture — that is, after sbt/sbt-eclipse@b6b0379#diff-e127bb09dd9d0b8de01cd7be195d59bcR30. This is just a first hypothesis, since I haven't rebuilt a single line of code. But anyhow, with the info I have this looks like a SBT bug.