cleanup layered soil example using helpers and substructuring module

LDDsimulation/domainSubstructuring.py

...ti-patch/layered_soil/TP-R-layered_soil-all-params-one.py

...l/TP-R-layered_soil-g-but-same-perm-coarse-dt-longterm.py

...i-patch/layered_soil/TP-R-layered_soil-g-but-same-perm.py

...se-Richards/multi-patch/layered_soil/TP-R-layered_soil.py

...esh_study/TP-R-layered_soil-g-but-same-perm-mesh-study.py

...h/layered_soil/mesh_study/TP-R-layered_soil-mesh-study.py