For the vast majority of users, the Eclipse plugin simply works, and I am a bit at a loss now as to what might be the problem in your case. Maybe someone else has other ideas?
In any case, your web.xml must refer to your widgetset as explained in the add-on use instructions - otherwise it will not be used even if compiled.
The file RefresherApplicationWidgetset.gwt.xml is the “widgetset fragment” of the Refresher, not a directly usable widgetset. Your own widgetset is effectively a list of such fragments to use (including the one with all the default widgets), and possibly some additional configuration. The “master” widgetset you want to compile in Eclipse must be directly in your project - not in a JAR. On the other hand, the fragments in the add-ons you depend on can and should be in their original JARs with the relevant metadata.
To manually compile the widgetset, you could e.g. adapt the
Ant scripts used by NetBeans
.