Modified data.py for command line args

Added the command line argument stuff to data.py as well. This impacts the
reference building command for the AIA file processing, which was outlined in
a previous commit.

I noticed that the command line arguments were going to be the same as for
calibration.py, so I added the argument parser stuff to gcms.py. Now there
will be a unified location for these commands.
Modified argument parser for calibration.py

In the last commit, I moved the argument parsing stuff to gcms.py, so that it
would be more global for other scripts. I modified calibration.py so that it
uses the argument parser from gcms.py rather than a local copy of the code.

Otherwise, everything else works the same.
Fixed some problems with data.py HDF5 file

The script data.py was generating a HDF5 output file that contained too many
columns of compounds. It was making columns for reference spectra files, even
if they did not have corresponding calibration information. I modified a
couple sections of this script to generate the columns from the calibration
data file instead, so that these files would contain info for the same
compounds.
Added warnings to data.py

Added a couple of warnings to data.py about discrepencies in background
subtraction between the calibration runs and the data files. This may not have
any affect on the final values, but it is good to know.