Managing Custom Code Modifications for WordPress Plugins

The number of custom modifications I am making to popular existing plugins has been growing to the point where managing them has been difficult. I have kept a list of what insertions or edits I have made in what files at what lines, but this is a bit cumbersome.

The problem comes when I upgrade my plugins and it overwrites my changes which I need to re-apply.

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Does anyone have an automated or at least, managed approach to this kind of code merging problem?

I feel like there is a GIT solution here, but I am not clear how it would be setup.

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