Maven clover2:setup triggers duplicate class exception

We have several maven projects that have more than one source directory. The non-default directories are added using the build-helper plugin. The clover2:setup goal instruments all source folders, but then sets all non-generated directories as source folders on the maven project. That results in compile errors, since source files are both present in the clover instrumented sources and original location.

Example:
java/src << 1. default source folder
java/src-build << 2. additional source folder
target/generate-sources/jaxb << 3. generated source folder

Case (2) is causing problems.