Re-implement ChemFlow config file, start with ScoreFlow.

[diegoenry]

I suggest to start by AMBER parameters.

1. ChemFlow --write-config to write a configuration file.

2. Something like ChemFlow --config project_protocol_target_chemflow.config should be enough to run.

3. Include ALL mandatory parameters such as --recetor, --ligand. and short comments about their need.

4. After running a WorkFlow, make sure a new configuration file is written, with all used parameters, including defaults.

Make all combinations in the GUI are covered !