create workflow documentation/diagram(s)

Understand the work flow of the MDANSE program and create workflow documentation/diagram(s) for it. It should be understandable for beginners of the technique.

Start by tracing the MDANSE program workflow and identifying the major steps a beginner needs to understand. Create workflow documentation and diagram(s) covering that flow, then check that the result is understandable to beginners of the molecular-dynamics analysis technique.

Written by the indexing model from the issue text.