[lohedges]

Closes #258.

For ABFE bound legs and ring-breaking perturbations, the Boresch and Morse restraints were only generated when restraints was None. Passing any other restraint, e.g. a distance restraint to hold a protein loop together, silently disabled them.

They are now generated unless restraints of the same type are passed, i.e. BoreschRestraints or MorsePotentialRestraints, and are added to any other restraints:

• The Morse restraints are added to config.restraints before the config is written, as before.
• The Boresch restraint is now only added to the dynamics restraints, not to config.restraints. It is generated after config.yaml is written, so storing it in the config would make the restraints in the config file and checkpoints differ, which would break restarts. It is still saved to abfe_restraint.s3 and reloaded on restart.
• Boresch generation is shared by the regular and replica exchange runners through _add_boresch_restraint().

The README now states that a Boresch restraint is always used for the bound leg.