My saves folder looks weird now, what happened?

The Compilatron's Error scenario is scripted to autosave more often if you have autosaves enabled. These autosaves are placed in a separate folder structure inside the saves folder, which can be navigated in-game by double-clicking the "Compilatron's error - autosaves folder".

The biters attack so quickly and I have no recipes to defend myself. What do I do?

While you may not start with a gun right away, you do have bare fists to pummel with. That said, melee engagements may not always be the way to go.