Intellij SBT Integration does not support source files in the SBT base directory

Hi, I have hit a problem with the Intellij SBT integration.

SBT projects allow Scala source files located in the SBT project base directory ( I have to work with some multi-projects where this has been done.

However, this seems unsupported by Intellij. Whenever I try to navigate to a symbol in a source file in a base dir, it does not resolve it correctly.