Hi Niels,
If the JNI libs are the only architecture dependent stuff, we should probably split the package (i.e. eclipse-cdt-jni and eclipse-cdt or so). That will also save the "mkdir/mv/rm"-code since javahelper would then install all the plugins into usr/share instead of usr/lib.
I split the package into eclipse-cdt and eclipse-cdt-jni. Jakub