Eclipse WTP "Java EE Module Dpendencies" not saving, or persisting

OK, I fumbled with the "amazing" Eclipse WTP project with the nice "Java EE Module Dependencies" option. There were a few projects that I just couldn't add them as dependency Java Utility Project to the web project. They were working before (for nearly two years;)). Apparently (as svn log says, nick), nick's cleanup effort two weeks ago removed some needed "nature" setting in .project file of those projects.

The solution was simple indeed. Just add this nature to the .project file of the Java utility projects:

<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>



Here goes over 8 hours of my time;). And, here are my two wishes:
1. Eclipse WTP should really give a warning if this nature is missing. Currently, there is no warning whatsoever. This is very bad, verrrrrrrrrrrry bad.
2. nick can do more meaningful work, than messing around setting like this;). (No offence, nick:)).

As far as the nature goes, you may also need this nature:

<nature>org.eclipse.wst.common.project.facet.core.nature</nature>