Fix issue #243

[lohedges]

Closes #243. The GCMC end-state topologies, which include the additional waters, were only written at the final checkpoint, so the output directory held a topology without them for the whole run. That didn't match the trajectory or checkpoints of a run in progress or one that had crashed. They're now written at the first checkpoint of each run, using a flag rather than the block number so that restarts are covered too (the cause of #87), and again at the final checkpoint so that the PDB files hold the final coordinates. A GCMC restart also no longer overwrites existing topologies with ones that lack the extra waters, which previously happened when a restarted run never reached a checkpoint, e.g. because every window was already complete. Additionally, the PME parameters read on restart are now logged in the same format as when they're tuned, rather than at full precision.