https://wiki.debian.org/UsingQuilt but the short form is that you keep the original sources untouched, then as part of building the package, you apply everything in a `debian/patches` directory, do the build, and then revert them. Sort of an extreme version of "clearly labelled changes" - but tedious to work with since you need to apply, change and test, then stuff the changes back into diff form (the quilt tool uses a push/pop mechanism, so this isn't entirely mad.)

Ha yes that does sound mad. If only there was a version control system specifically designed to track changes to code...