Revert "Revert "Various misc changes that still need additional testing. (This commit might be reverted pending additional testing and development in another branch.)""

This reverts commit d4f5ba21df2c361f41425ecad87e37a5570dde42.

Conflicts in pydpiper_apps/minc_tools/registration_chain.py were manually resolved.

NOTE: Having to revert the revert is ridiculous. I'm not sure why this didn't work properly the first few times w/r/t branching and merging. FAIL.