sbteclipse expects all source folders to be local to the project:
There is a feature in Eclipse called linked resources to support external source folders. This requires additional information in .project:
I have a patch for this, submitting shortly (although the link names are a bit ugly....)
Fixes #136 - Support for non-relative source directories.
* Adds a splitting function to srcDirectories when generating project files.
* Generate link name based on *absolute* canonical path of a resource