I noticed the find usage and goto source features of Netbeans fail to work after the recent move of some JavaFX projects from rt-closed to rt. A further investigation found that the information in project.properties of these projects were gone. As Kevin pointed out that the information in How to Open Source JavaFX wiki is incorrect:

11. In project.properties, replace javac.classpath to just refer to ${JFXRT_HOME}/jfxrt.jar. Make sure to define JFXRT_HOME in project.properties if not already defined.

It shouldn't be "replace" but "append".

I'm attaching a patch that will address some of the issue that affecting my work. There is still other problem such as most of decora projects are now in red I have yet to figure why.