You may have a look at Quilt. I doesn't solve the problem the author described but may help you once you accept there is no easy solution in sight.

Quilt is automation for the "bag of patches" model. I used it once when I needed to upgrade the internal bag of patches at $big_corp so as to apply them to a newer version of $public_app. It was predictably complex but somehow still manageable.

If you squint a bit then the [bag of patches] + [automated application in order] is a poor man's Git. If you keep this in a git repo then you're basically versioning repos (poor man's ones) in a repo. It almost sounds like the solution to author's problem :)