Add compileOrder into the org.scala-ide.sdt.core.prefs file

(New) Fix to honor the compileOrder := CompileOrder.JavaThenScala directive in the build.sbt, Re Issue: #218

Since sbteclipse plugin & ide uses CompileOrder.Mixed as a default, I'm effectively filtering that value out, so we only write a value (or a file!) if its one of the other two settings.  I also split out the code to separate it from scalacOptions