Hold project references on Gradle classpath container rather than on the project classpath.

After applying this change, project references are held on the Gradle classpath container rather than added as project references to the project itself to avoid changes in dependencies causing undesirable changes in .classpath.

This is preparatory work in an effort to allow portions of multi-module projects to be included in an Eclipse workspace, where project references to subprojects that are not open in the workspace are substituted with jar entries representing those subprojects.

I put some thought into what to do about projects that use the existing plugin, and for which the existing plugin has already added project references to projects.  However, since these references are not easily distinguishable from those that the user may have added manually, I can only think to leave it up to the end user to clean up the remainder.