Improve CLI

[talagayev]

Describe the feature you would like to have

Currently we have 3 entry points, that we are calling with openmmdl_setup, openmmdl_simulation and openmmdl_analysis

Overall we can improve the structure, add an cli.py to make them in one place and make them have openmmdl to have help and then do openmmdl setup openmmdl simulation and openmmdl analysis

Additional context