It's good to know that you are aware of the pitfalls.
Still, I'd recommend that you use a VCS (git or mercurial) under the hood for this. They are optimized to store and retrieve previous versions (that is their primary job after all), they give you tools to compare versions, and they give you context for each version you commit (or your module commits).
Yes, you could say that you don't really need all that, you just need something that hides and automatizes that mv results.txt results.txt-5 step, but little projects like this tend to accrete features and use cases, and before you know, you're stuck with an underdesigned, metastatised monster of a system.
