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patch-package is a tool for this specific purpose

You commit your changes as a diff text file and add the patch-package command to your post-install hook so it runs after every install

My main use for it is fixing other packages' package.json exports field and Typescript definitions

Interesting, I can definitely see this being particularly useful for typescript fixes.

Where should one put the text files in the code base? Do you create some root level "patch" directory?

patch-package automatically makes a `patches` directory at the top level of your project with `{package-name}+{package-version}.patch` files in it.

yes