Many changes!

Hi Sophia --
I did a lot of messing around today but I think everything still works. Most important changes:
- made a log file which records the command-line parameters
- changed how multi-extension FITS files are read in (now it takes the first SCI extension after the primary, or the first extension if none are named SCI). Also, when looking for WCS information in a multi-extension file it uses the first SCI extension (as above), rather than the primary. This was needed for some MIPS data.
- changed how datacube is written out (now it has useful header info, and is multi-extension rather than 3D -- can change this if you don't like it)
- either arbitrary rotation angles, or PA of the reference image. I tested this on some Gemini data that was "left-handed" (ie north-up, east-*right*) and it still worked, to my amazement
- added quite a few more comments and cleaned up the code a bit. I have some ideas for other changes that could be made and will enter these as issues.

What I haven't done:
- anything to do with the flux conversion database
- anything to do with kernels
- documentation (including providing test data) other than code comments