[lohedges]

SOMD2 always applies ghost atom modifications with the default ghostly options. This adds a way to tune them, and guards against applying the modifications twice.

• Add a ghostly_kwargs option that passes options to ghostly.modify. It takes a dictionary from Python or a YAML config, or key=value pairs on the command line, e.g. --ghostly-kwargs k_soft=3 stiffen_rotamers=true. Values are parsed as YAML, and keys and value types are checked against the signature of ghostly.modify, so new ghostly options need no changes here.
• The options are saved with the config, and changing them on restart raises an error.
• Systems already modified by ghostly raise an error unless ghost_modifications is disabled, which uses the existing modifications, or force=True is passed in ghostly_kwargs, which applies new modifications on top of them.
• A warning is logged when ghostly_kwargs is set but ghost modifications aren't applied.
• Added tests, plus README and CHANGELOG entries.

Requires OpenBioSim/ghostly#20.