[WIP] Revision to Thermo target

Progress:

- Parser for new data format (75% done)
- Map observable names to simulation chains
- Specify all simulation options in input file parser
- `md_chain.py` runs general simulation chains
- Time series class; Split `get_timeseries()` from `molecular_dynamics()` 
- Apply MBAR estimator for grouped thermodynamic state points
- Calculate observables from time series
- Multiple initial conditions
- Map abbreviated units to full units
- XML format parser