Remove managedSourceDirectories modification

This fixes adding correct source directories to Idea project files with
sbt-idea plugin version 1.4.0+. 

Plugin authors should not modify 'managedSourceDirectories' directly, 
but only provide 'sourceGenerator' which generates sources under a 
subdirectory of 'sourceManaged' setting of the scope as described here:
http://www.scala-sbt.org/0.12.3/docs/Howto/generatefiles.html