Change utilities and angle namespace; cleaned up some basic formatting
Changed material namespace
Changed geometry namespace and fixed some formatting
Moved external sources to new folder, namespace; tested with slight mod to interface.  Now, iso and discrete require the fine mesh map, which suggests some helper functions in Python if needed
Shuffled equations and boundaries to separate folders (same namespace); code cleanup and such
Switch Mesh side name convention to west, east, etc.  Stub boundary tests.
Added adjoint flag to quadrature
Now equations request angles for the true octant.  This is required for adjoint computations.
Updated transport routines for new namespaces and such
Updated transport for new namespace; cleaned up some utility typedefs
Finished namespace switches and general code cleanup: verified test suite
Finished swig update for the new namespaces
Switch return of boundary creators
Switched back equation octant to 0
Moving diffusion over to solvers.  Base operator and vector in place
Stub for diffusion boundary
Added diffusion boundary and fixed SN boundary bug that had yet to surface
Stub diffusion fixed source solver
Further diffusion stuff
Diffusion operator bug fix