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I have a git branch where I apply my patches. If the master branch is updated I pull their upstream changes and then rebase my commits on top of theirs [1]. Once in a while conflicts may arise, but they’re usually solved easily.

[1]: https://dwm.suckless.org/customisation/patches_in_git/

I think part of their ethos is that they don't like scale. They like small. It's a feature, not a bug.

Provided the source is reasonably organised the configurable variables etc are likely separate enough from any code you would care about patching.

Patch applying is quite robust, you do not need the code to be identical, the line numbers don't need to match exactly, it's most sensitive to the few lines of context.