Add equilibration step to RBFE protocol or "equilibration pre-processing"

[IAlibay]

From @hannahbaumann

We should try to do an extra equilibration for our RFE protocols.

We could run a standard equilibration on the system after creating the HTF (could just add it as a step ~ https://github.com/OpenFreeEnergy/openfe/blob/915d11022c31ce5e6835aa220965eb6c5698f794/openfe/protocols/openmm_rfe/equil_rfe_methods.py#L964 and then update the positions in the HTF object).