MeshRegion refactoring

[johnomotani]

The MeshRegion class includes methods that calculate geometric quantities for the standard BOUT++ locally field aligned coordinate system. Ideally MeshRegion would be generic, with the BOUT++ specific parts separated out into a derived class, e.g. BoutMeshRegion (which would then be created by BoutMesh). At the moment the only use of hypnotoad is for BOUT++, so this is not a priority at the moment.