After Eclipse resolved some of the bugs with modular projects it became easier to finalize the repository settings. The affected projects are 'apps' and 'buildSrc'. The Wiki will be updated accordingly.

* The folder "rt/buildSrc" is defined as an Eclipse project, but it probably does not make sense since it is a Groovy project and is not used in normal development. The Eclipse files should be removed from this folder. Anyone who wants to work on it can import it ad-hoc.

* The "rt/apps" folder is defined as a gradle (sub) project and as a Java project. "apps/toys" and "apps/samples" are also Java projects without any of their subdirectories being projects. It seems that the correct configuration is to have a Java project for each app under the subfolders of "apps" (toys, samples, performance and test); remove the project configuration from these folders; and make "apps" itself a dummy project so that gradle is satisfied.
This will create many new projects in Eclipse, but the clutter can be handled via Working Sets.