Added the Non-hydrostatic mountain test. The code seems to be broken for
the topography test cases at this commit.
Added InertiaGravityWaveTest
Added discussion of vertical coordinate to implementation document
Merge branch 'master' of https://github.com/paullric/tempestmodel

Conflicts:
	test/Makefile
BUGFIX: Moved Coriolis evaluation to EvaluateTestCase() in
GridPatchCSGLL.cpp
Ignore mountain wave executables
BUGFIX: Changed how NoReferenceState is handled in cubed-sphere tests
- Added diagonal width for 5th order vertical
Changed how reference state is handled in InertiaGravityWaveTest
- Added FullyExplicitVertical option to InertiaGravityWaveTest
- Changing the Earth scaling radius now affects hyperviscosity
reference length
- Added temperature as an output quantity
BUGFIX: Initialize m_fOutputTemperature in OutputManagerReference
Switched all test cases to use TimestepSchemeStrang instead of
TimestepSchemeARK4
Added tracer support
- Moved ApplyDSS to PostProcessSubstage in Grid
- Added note that DIFFERENTIAL_FORM does not guarantee mass
conservation under the current topography formulation