Shut up warnings in BoussinesqBuoyancySPGSMStabilization

This is related to #93. In particular, I was playing with including
some additional terms in the Boussinesq buoyancy that pop out for
SPGSM/VMS stabilization, but they seemed to do weird things, so
left them commented out. The things that were getting unused warnings
are related to that so I left them in there commented out for whenever
someone has time to look at this.
We're not computing Jacobians (yet) in ReactingLowMach

So throw a libmesh_not_implemented() in there.
Get rid of unused dof_indices in ScalarODE
Shup unused variable warning
Shut up comparison warning
Shut up unused variable warnings
Shut up unused warnings in Cantera tests
Shut up unused variable warning
Silencing uninitialized variable warning.
Unused variables in ICHandlingBase
Updated CHANGES for 0.4.0 release.

This is likely not complete (> 1000 commits since 0.3.0... fail!),
but hits many of the major things.
Merge pull request #165 from pbauman/0.4.0-release

More 0.4.0 release prep