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When a UML model contains more than one root Element, only the first one is displayed in the ModelExplorer. This case cannot be reproduced directly with Papyrus, as it only allows one root Element (as well as the Eclipse UML2 editor).
Fixed in a1e7917d80a2548ff3076f0a38f3e5c8995da27f All the root UML Elements are now displayed in the ModelExplorer. Stereotype applications are still excluded.
When a new root is added, the ModelExplorer is not refresh. This is due to the roots being computed only at the creation of the ContentProvider, and cached.
Fixed in Bug 366029