UpdateEclipseClasspaths is putting duplicate entries into the generated .classpath files that result in name conflicts.
Not sure why, but sbt compile updateClassifiers results in duplicate jars in the lib_managed bundles and jars sub-dirs.
On my system, there is also a spurious duplication of the scala-xml library (version 1.0.4 AND version 1.0.6 are found under bundles/org.scala-lang.modules). It's not clear why this is happening.
Tool needs to be fixed to avoid the duplicates, and the .classpath files of all the eclipse projects fixed to not have the duplicate entries.