[lohedges]

Closes #254.

When replica exchange re-uses OpenMM contexts across lambda values (max_contexts less than the number of replicas), every replica built its own equilibration and production dynamics objects during setup, each thrown away when the next replica took the context. Minimisation and equilibration now work per context instead: each context builds one equilibration and one production dynamics object, and its replicas are run through them in turn. With max_contexts=1 that is two builds rather than two per replica.

• Equilibration no longer advances a replica's clock, which is restored afterwards rather than reset by building a new context.
• A rebuilt context, or one left in a bad state by a failed minimisation, is set up in full the next time a replica is loaded into it, including its lambda value and GCMC water state.
• Failing to create a dynamics object during setup is now reported as such and stops the run, rather than being logged as a minimisation warning.
• Removed some unused attributes and duplicated setup logic.