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I use undo-tree mode in my emacs setup. Every once in a while, after writing a lot of text, I accidentally undo changes while I have some region selected. I am not 100% sure what undo-tree is doing and this is not 100% reproducible but there is high chance that this completely messes up my text. If I visualize the undo-tree I see a linear path but I cannot go up the tree even a single node (emacs just hangs).

Any idea why this is happening? I suspect that undo-tree is trying to undo the changes in the selected text as opposed to the whole buffer. If that's the case, can I disable this behavior?

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To disable undo/redo-in-region as to the library undo-tree, set the variable undo-tree-enable-undo-in-region to nil:

(setq undo-tree-enable-undo-in-region nil)

The doc-string for the variable states:

When non-nil, enable undo-in-region.
When undo-in-region is enabled, undoing or redoing when the
region is active (in `transient-mark-mode') or with a prefix
argument (not in `transient-mark-mode') only undoes changes
within the current region."

The author of undo-tree (Dr. Toby Cubitt) admits that undo/redo-in-region has always been buggy and difficult to debug. He suggests disabling undo/redo in region until he has free time at some point in the future to work on this library again. To read about the most common bug with undo-in region, see the following two bug reports:

https://debbugs.gnu.org/cgi/bugreport.cgi?bug=16377

https://debbugs.gnu.org/cgi/bugreport.cgi?bug=16523

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