Pruning submodule directories
closes #3853
Skip thermal term in J if material property for it doesn't exist ref #3807

This fixes a test we inadvertently broke in Marmot.
Merge pull request #3854 from permcody/prune

Pruning submodule directories
Merge pull request #3856 from bwspenc/j_thermal_term

Skip thermal term in J if material property for it doesn't exist