Bug in Nautilus: 1. Pharo Image
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What you describe is a bug of cmd+r refactoring. Because it not works when you press it on message selector for example. Instead of method rename dialog it will try to apply variable rename refactoring. And I see now that it implemented in the way to work only for temp/arg variables. So cmd+r on instance variable will also not work. To fix it we should delegate refactoring to selected node itself. Look at #renameTextSelectionForMethod method.