Fixed OS dependent naming of extracted flat files

OS X seems to use the whole APID table name, while *nix scrunches it. Now
we check in the output of dohydra to see what the file was called.
flatfu now also saves master flat name with correct apid scrunch
Oops, fixed index error in previous commit.

This is why you test the entire pipline before commiting code
Added option for a throughput file

Use -r flag for some reason
Flatfu now figures out final scrunched name in real time.
Fixed bug where IRAF's own normalization screwed up stiched image.
Renormalize stiched flat to be consistant with IRAF msresp1d