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 (https://www.scala-sbt.org/1.x/docs/Howto-Customizing-Paths.html#Disable+using+the+project%E2%80%99s+base+directory+as+a+source+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.