Update or remove analysis notebooks for ABFE and SepTop?

[IAlibay]

Now that the CLI does gathering, would it make sense to either remove or update (to use the CLI methods) the ABFE and SepTop "analysis of results" notebooks?

[IAlibay]

Thoughts @atravitz ?

[atravitz]

My ideal solution is to update the notebooks, but have a note at the top saying "you can do this with the CLI now" and point to those docs. I've been asked before by users "how do I do openfe gather using the API?", so I think keeping these examples up is a good idea.