Testing cartesian mesh idea
Moved helper mesh classes into CartesianMesh as simpler structs.  Modified tests to reflect this change.
External source updates for new geometry
Simplified some swigging, and have what appears to be a real solution for petsc initialization and finalization from python.
Testing cartesian mesh idea
Moved helper mesh classes into CartesianMesh as simpler structs.  Modified tests to reflect this change.
External source updates for new geometry
Partial update for SWIG treatment of SP based on the boost shared_ptr macros.  Updates several tests to use the new Callow initialization singleton, which eliminates needing secondary scopes.  Small cosmetic changes throughout.
More cleanup and callow init switches
Initial boundary mods
More work getting geo into place
Modifications to transport and geo packages for geo updates
Merge conflicts from dev rebase