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The refactoring and the search tools are only reaching the classes that are opened to edit. If there is a reference to the class A in a class B, but this class B is not open to edit, then the refactoring and search will not see this reference. It seems that the workspace is limited to the open files. This behaviour was not happening from the first. But I don't remember an event that could cause the problem.
No, this shouldn't be the case. What happens is that the JavaModel actions are now aware of possible editors with unsaved changes (shared working copy notion), but other units are still visible. Do you have steps to reproduce ? We aren't aware of such an erroneous behavior.
Closing, please reopen if steps can be described.