Major change in code internals

Hi Sophia -- I was trying to use imagecube with Sahar's data and not being very successful. For what I needed to do, a different file structure was necessary, so I rewrote the code to have 2 output files: a multi-extension FITS file which contains the processed images, and a separate 3D datacube file (see OUTPUT in the help for the main imagecube file). This makes it easier to run one task at a time and also allowed me to simplify the code somewhat. I put in a few more bells and whistles, like adding information to HISTORY cards in the header.

You may want to have a look at the changes in detail (you could clone my file_struct branch if you like) before merging. We can also talk about it over Skype if you like..