Restructuring filesystem for cleanliness

[StripedMonkey]

As it currently stands there's lots of random files that don't belong. Cleaning these up would be nice. My biggest question is how best to organize stuff.
My initial thought is that every object seems to have a material, script, mesh, etc. so taking each object and putting it into a single file with all the materials related to that. The issue becomes that there is a lot of psudo-junk that is a mix of everything so it becomes difficult to sort (Ex. wipmesh.tscn is unused at this point it seems)