When you start a JustCode multi-step refactoring the Undo enters transactional mode, i.e. all the changes made to the file during the refactoring are a single Undo transaction and the Undo toolbar is disabled while the refactoring is in progress. If you chose to commit the refactoring (that'd be press Enter for Extract Method) you get the Undo toolbar enabled again. If you click Undo at this point of time ALL the changes made by the Extract Method will get undone at once. If you chose to abort the refactoring (that'd be Esc in Extract Method) ALL the changes made by the Extract Method will get undone and the Undo toolbar will get enabled again.
Is this how things work for you? If not could you let me know at what point the VS behavior deviates from the described procedure?
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