Late-stage files now have independent arg-handling and regSpec path generation.
PrepSpec done for main bases. A few more things for health guys.
Consolidated pre-clean5 stuff for oshpd into clean1.
Clean 5/6 now handle basic health specs.

This is a combination of 3 commits.
The first commit's message is:
Clean5 works with patients and simple zip-level stuff.

This is the 2nd commit message:

Changed the naming scheme and variables for airQ files.

This is the 3rd commit message:

clean5 and 6 should work with all bases
Regs now handles bases, but health data not ready.
Overhauled diagnosis tags, now ready for regs.
Finished debugging the basic health stuff, so should be done.
Merge branch 'reg-env-1410' into develop