[Discussions] How we define endstates

[IAlibay]

Background

Current Protocols define ChemicalSystems for stateA and stateB in the following manner:

The ask

We want to align how we define states for Protocols so that we have a consister manner of pull out relative and absolute transformations from AlchemicalNetworks.

The move recently has been to promote how SepTop & AFEs do it, but we should discuss how we want to do things going forward.

The questions

1. Is the SepTop & ABFE definition suitable?
2. Are there any issues with them (performance, comprehension, etc...)?
3. What other ways could we define the end states?