Via the "Project archives" view i configured two archives to be created:

--application-ejb.jar
--application.ear

The application-ejb.jar holds most of the java-classes and will be created into a sub-directory /library. In this directory you wil find additional other application-relevant libraries too.
The application.ear will zip the whole contents of /library-directory to an ear-file and save this ear under a directory /release.

So far so good, the project has now assigned the JBossIDE Packaging Builder to it's builders. If i now make a Project-->clean from eclipse, then not only the application-ejb.jar will be deletet (as i would expect), but also the wohle other libraries and files and even all "hidden" informations, like .svn-subdirectories in directory /library will be deleted.

This is definitely not the correct handling of cleaning the archive-files. The project is after such a clean badly damaged and can only be restored by a fresh checkout.