So I know nested prefabs aren't supported..

So how would you go about managing prefabs that need to contain other prefabs?

For instance. Let’s say I’m making starfighters out of several components. I have cockpit prefabs, engines, weapons, hull sections. All prefabs. So I assemble a starfighter, and I want to make a prefab out of the whole thing.

Since prefabs don’t support this sort of thing. How would YOU go about doing it?

I’m aware of some of the “nested” prefabs packages, but I want something free and future-proof.

yes u can. or at least i can. just pull every part to ur scene/hierarchy asambly all the part togethers . make a new prefab. and just make it a prefab all together. idk if i explained myself. hope u understood.

“How would YOU go about doing it?”
So i just implement this by myself)
http://forum.unity3d.com/threads/236719-Prefab-Evolution-Plugin?p=1572475#post1572475