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After a new customization application, the model explorer is not refresh (understand its appearance is not modified). The appearance change when a modification is made on the model (ex: create a new element).
This happens too when some modifications are done in the sequence diagram. For example when resizing a combined fragment, the enclosed fragments are updated but sometimes it doesn't appear in the model explorer. A save or the creation of a new element refresh the viewer and "fix" the problem.
Commited a small fix for the refresh of the Model explorer in order to refresh the content and the display when applying new customization. A wrong instanceof test was performed, relying on the old architecture. I don't think this will fix Mathieu's problem.
it seems to be fix by fixing bugs on overlay of facet (done in the revision 3945)