I've now split this into pre_mol_commands and post_mol_commands, which is what I was originally thinking of doing. The pre_mol_commands can be used for adding things like custom parameter files, whereas post_mol_commands can be used for anything that needs to reference the molecule itself.

This changes the API, so I should really do this as a feature. The issue is that the current 2023.4 implementation is broken, so I do need to apply a fix there. Should I just revert the functionality there, i.e. move the position of the leap_commands? It would be a shame to need to apply this twice.

Just revert to the old behaviour is good with me.

@chryswoods: Do you have any opinions on how to proceed? Should I merge this as a fix and backport to main as is, or merge as a feature and apply a separate fix to main. I don't think anyone is using this feature other than Exs and I assume that they are happy as long as it works. Given that the custom_parameters functionality is broken, I don't think anyone can be using it. (No reported issues.) If I were to apply a different fix on main then the easiest thing would be to remove the custom_parameters option entirely and revert the position at which the leap_commands are injected. (Annoying, my new solution is what I had originally proposed.)

I think this can classify as a fix, so you can put it into the BioSimSpace patch release. It's at the borderline of being a feature, but if it isn't in widespread use, and we want a stable last patch while people play with 2023.5.0, then I think it is worth merging as a fix.