Seed perturbed coords from a system clone, not raw arrays#140
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This PR improves the setup for the
perturbed_systemoption used for multiconformational seeding. Instead of apply the positions and periodic space of the perturbed system to the OpenMM context post setup, we instead set the positions and space of the input system prior to setup. This means that the setup pathway is the same, regardless of the input, so that GCMC waters and virtual sites are added afterwards, i.e. we don't need to account for their presence when setting the positions, which required padding arrays, etc.Note that this change needs the latest development version of Sire.