So I have this mod manager for Elder Scrolls: Oblivion that sets up a virtual filesystem as an overlay over the game's original directory structure, and then launches the game in a way that makes the game see the overlay as if they were the original files. I am very impressed at what seems like outright computer voodoo, I had no idea Windows had those kinds of APIs or that kind of capability.
I don't know how this tech works but I feel like we could have had this already using the tech I described above.