Use shared_ptr for Mesh in MeshFunction.

Need to look into SWIG ignore for reference constructors.
Moved ignores for Mesh references to macro and added template parameters.
Resolve memory issues with Mesh in MeshFunctions via Python.
Fix for MeshFunction::mesh change in Exodus.cpp.
Fix and update a doc script for git transition. Fixes issue #27.
Fix table rst formatting.
Fix another rst table for formatting.
Use MathJax via Sphinx for scalable maths in docs.

Requires Sphinx >= 1.1
Set minimum Sphinx version in conf.py.
Merge branch 'garth/doc-fixes'