Added base variables for anelastic mode
Anelastic buoyancy and pressure input, not a correct solver yet
Solved the anelastic pressure solver
Made the advection anelastic
Put the density in the eddy diffusion
Set the ghost cells for the reference vars
Fix the problem with the eddy diffusion by proper N2 calculation
Give the input file as argument to the thermo create function
Create the reference profile from the initial profile
Calculate the reference profile from the initial conditions
Merge branch 'thermo' into thermo2

Conflicts:
	include/thermo.h
	include/thermo_dry.h
	src/diff_les2s.cxx
	src/thermo.cxx
	src/thermo_dry.cxx
Compiling version of merged branch
Merged anelastic base state into moist thermo routine
Use the height varying reference buoyancy in the new routine
Merge branch 'thermo' into anelastic
Merge branch 'thermo' into anelastic

Conflicts:
	cases/bomex/bomex.ini
	include/thermo.h
	include/thermo_dry.h
	src/thermo_dry.cxx
	src/thermo_moist.cxx
Add the surface pressure to the drycbl les case
Remove reading of uncessary variable in thermo
Merge branch 'thermo' into anelastic
Merge branch 'anelastic' into anelasticmerge

Conflicts:
	include/thermo.h
	include/thermo_dry.h
	include/thermo_moist.h
	src/diff_les2s.cxx
	src/thermo.cxx
	src/thermo_dry.cxx
	src/thermo_moist.cxx