Enable reproducible restarts from stopped simulations

[orionarcher]

Currently there is no clean way to restart a simulation with the exact state from a previous simulation. This should be corrected.

[CompRhys]

Resolution strategy will be to address #19 and deprecate hdf5 for h5md assuming nothing adverse arises in doing so. Then we should be able to write a utility that will allow resumption assuming the PRNG state has been saved in line with #460.