This is the default behavior of sbt to have javaSources and scalaSources in classpath. Them being in eclipse is just a consequence.
It can be changed with (for only java project):
unmanagedSourceDirectories in Compile := (javaSource in Compile).value :: Nil
or (for only scala project)
unmanagedSourceDirectories in Compile := (scalaSource in Compile).value :: Nil
or just remove them all
unmanagedSourceDirectories in Compile := Nil
You can do it like this:
unmanagedSourceDirectories in Test <<= (sourceDirectory){ src => src / "somerandompathfortestsources" :: Nil}
To see what they are (in sbt console):
show unmanagedSourceDirectories
show sources
...
To see what makes them:
inspect unmanagedSourceDirectories
...
More about: http://www.scala-sbt.org/0.13.0/docs/Detailed-Topics/Java-Sources.html