What other choice is there if I want to maintain independence of hacks? If I just use plain diffs, how do I update my hacks when a new arc3.tar comes out and breaks them? Manually? That's even more of a pain.
I have some ideas that appear to be promising, but no solution to offer you yet. For example, I look at one of my patches and say, "why do I need a patch? Why isn't Arc hackable enough to let me implement this by just loading some code?" and, if I can, see if I can make Arc more hackable instead. And then, if it works, my patches become much smaller, just extending Arc to become more hackable instead of implementing my whole hack, small enough so that often the patch will still apply in new versions of Arc. Now when a new version of Arc comes out I don't always have to come up with a new patch, instead what I'm doing is simply testing my patches to see if they still apply.
