Documentation regarding input/output options

[ctk3b]

Current inputs can come from mbuild, parmed or openmm topologies + an xml file.

By default Forcefield.apply() yields a parmed structure but for users interested in running in OpenMM we can also easily break out earlier. This needs to be tidied up a bit and properly documented.

[mattwthompson]

We should probably add a page in the documentation that is clear about this; I believe we still only currently support those three formats, but that is likely to change in the future.