When any of the source dirs is external (example from the grails project):

sourceSets {
  main { groovy.srcDirs = ['../groovySrc'] }
}

Actual result:

The output .classpath file contains paths to 'external' folder, e.g. folder that lives outside of the eclipse project folder. Source directory references to external folders (both relative or absolute) are not supported by eclipse. Hence there are path errors when project is opened in Eclipse and user must fix them manually.

Expected result:

External source folders should be created in eclipse via 'linked resources' aka 'links' feature. Those linked resources are maintained in .project file. Then the .classpath should contain source folder reference to the linked resource. This way there are no path errors on project import and the correct sources are on the path.