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Let's say I am setting a variable to a value inside a hook. I'm hooking the hook to the minibuffer-setup-hook so that it runs whenever the minibuffer opens. Will the changes made by the hook persist after I close the minibuffer? Or will they revert back to their original state?

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It depends on what kind of changes you make. There's nothing special about code invoked from a hook.

If you set a global variable it remains set until something sets it differently or makunbounds it.

Your question is general, so the answer is general. If you pose a specific question, e.g. with some code, specific answers can likely be given.

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