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Some view parts are showing orginal element although there is a working copy. To make sure that a refactoring manipulates the correct Java elements the refactoring actions must map a original element to a working copy element if possible.
Done for extract method and self encapsulate field. Adam please check if all your refactoring work correctly on working copies. If so mark PR as fixed
fixed Pull Up and Rename Parameters i believe everything is working copy aware now if not - please file bug reports against specific refactorings