Improving handling of YAML

[aalexmmaldonado]

There have been some inconsistencies with the command line interface where we are unable to instantiate a class such as AmberTopoGen for the engine in SimlifyConfig. This PR introduces a root import YAML keyword so we can instantiate classes and set them on our SimlifyConfig. For example, we should now be able to include this in our YAML config files.

import:
  engine: simlify.simulations.amber.topo.AmberTopoGen

Fixes #12 #17

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[nacefguessaymi]

Looks like this imported the YAML file.
I think ff needs to be read from the YAML file as well. Still getting the AmberTopoGen has no attribute 'ff' error.