Major overhaul to alchemy.py, where a single alchemically-modified system is now created with alchemical parameters (lambda_torsions, lambda_restraints, lambda_coulomb, lambda_sterics).
Softcore Lennard-Jones and electrostatics are now used to allow lambda_coulomb and lambda_restraints to be modified simultaneously.
Some additional changes are needed to fully support decoupling and annihilation; no significant testing has taken place, except doctests.