Create flow diagram for MUSE

At the moment, the workflow of the program is obscure for end users, and even for developers who might need to improve and add new components. This task has as main priority to make this workflow explicit for all stakeholders.

It is split into the following subtasks:

- [x] #111
- [x] #112
- [x] #113
- [x] #114

The flow diagrams can probably be created by us, but documenting the scientific and numerical assumptions will need the involvement of @sgiarols .

Comienza revisando las subtareas completadas #111, #112, #113 y #114 para comprender el flujo de trabajo que documentan. Crea diagramas de flujo que hagan explícito el flujo de trabajo de MUSE y documenta las suposiciones científicas y numéricas con la colaboración de @sgiarols.

Escrito por el modelo de indexación a partir del texto del issue.