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I was experiencing freezes of sometimes up to 30 seconds about 3/4 of the the time when I used my muscle memory to hit "undo", which I do as part of my regular "kill-line undo" combo. Something must have changed recently because I started to have show-stopping freezes of my emacs thread when I tried a routine "undo." I finally managed to squeeze a `toggle-debug-on-quit` and, with a bit of patience, got a C-g in during the freeze. The culprit in the resulting stack trace was my global undo-tree mode, which in combination with my other settings must have started failing. I turned it off by removing the line in my init.el and also running `global-undo-tree-mode` to toggle the mode and&; far, no more funny freezes on undo. There are occasions when the undo tree is great and useful, but not at the cost of sometimes completely being a show stopper.

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