remove support for top-level source files

[cvogt]

This leads to problems in IntelliJ in particular, which does not support non-recursive source directories. This will lead to build files being located at build/scala/build.scala, which is a bit redundant, but is probably worth the resulting simplicity and uniformity of this change.

Related gitter discussion https://gitter.im/cvogt/cbt?at=5949f18fa44c60fa4c486e45