Use atom::create_clone for faster copying and cloning

[cgreenberg]

Can now copy States, Gaussians, and Representations, so this should be much faster than copying things at the python level.

We still do have to copy the information that's in the python classes, like the TempResidues etc (including assigning correct Tempresidue.hier) so it's not that simple. And this won't work on create_copy since it's not identical. BUT it could be super helpful if you simply want to clone an entire state - which is a common crosslinking situation.