The main Class must be fully qualified with the package:
Compile/mainClass := Some("myPackage.aMainClass")
This will work for run and it will set the Main-Class in the Manifest when using the package task. The main class for these tasks can be set separately as in:
mainClass in (Compile, run) := Some("myPackage.aMainClass")
mainClass in (Compile, packageBin) := Some("myPackage.anotherMainClass")
Note:
mainClass := Some("myPackage.aMainClass")
does nothing. If you put this in your build file you will receive no warning that it does nothing.