Seperate concerns of loading simulations, running dynamics, publishing frames, listing simulations in omni

> Right now Simulation represents both the necessary state of a loaded simulation, and the stub of a simulation that could potentially be loaded from a file for the sake of the Omni runner--these should be two independent things. Doing this would remove the need to assert that certain state is not None (anything that would be loaded later from the file).

Start by locating the Simulation implementation and the Omni runner, then trace how loading, dynamics, frame publishing, and simulation listing currently share that object. Identify the state that belongs to a loaded simulation versus a loadable stub; done means those responsibilities are independent and no longer require assertions for state loaded later.

Written by the indexing model from the issue text.