Make update-files less destructive

[martinthomson]

There are a few places where changes to files need to be preserved.

• Makefile (really, we just want to preserve the part from "include" to "endif" and leave the rest alone.
• README.md (maybe; this is hard)

.gitignore is already something that is handled. Maybe model the process on that.

[martinthomson]

I've made some changes here on the Makefile side of things. It's a lot more fiddly than I might have liked, but I think it's more or less where I'd like it. Next: README.