When Emacs sporadically pauses for long periods of time (over 5 seconds). During that time, the GUI is unresponsive, but it queues up whatever I’ve typed and executes it as soon as the pause is finished. The couse is savehist-mode activated and that saves the minibuffer history every 5 minutes. To slove this issue the best way is to turn it off. The history file can be huge (400 MB sometimes more, like 5GB). Just delete the file and start over. Check inside your ~/.emacs.d.

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Reference:

1. savehist-mode

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