clean up two-phase examples by making use of helpers and substructuring module

...e/Archive/TP-R-2-realistic-parameters-densities-scaled.py

...P-R-two-patch-test-case/TP-R-2-patch-pure-dd-realistic.py

...wo-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd.py

...TP-R-2-patch-realistic-gravity-but-same-intrinsic-perm.py

...-patch-realistic-no-gravity-but-varying-intrinsic-perm.py

...h-test-case/TP-R-2-patch-realistic-same-intrinsic-perm.py

...-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic.py

...s/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-test.py