Added more command line arguments.

I had user defined values in both data.py and calibration.py that
were identical, so I added them as new command line arguments. Refactored
these two scripts to take that into account.

There was one small change made to data.py that was a result of the last
commit where I changed how the fitting was done.
Refactored calibration.py

I refactored calibration.py in order to make it easier to modify in the
future. More things are factored into functions.

I also made it so that there is only one csv file with reference information.
This removes a lot of the files that were laying around in the directory.
Single reference text file

Modified the text reference file processing functions to use a single
reference txt file.
A few more modifications to calibration

I needed to add a few more values to the HDF calibration file. This required a
bit of modification to a couple functions.
Added internal standard fitting to calibration.py

I made some modifications so that internal standards can be used for fitting
with my calibration script. This required some new command line arguments as
well as some additional code. Several new parameters will be stored to the HDF
calibration file.
Added internal standard cal to data.py

I modified the data processing script data.py to be able to handle internal
standard data.
Modified background addition

The background was being added directly to the reference array, but all other
mass spectra were being normalized. I normalized the background addition so
that the fit data were more consistant with one another.
Small change to plots from data.py and integration

Changed the plots from data.py so that they plot the fitted GCMS lines rather
than the fit coefficients from the NNLS fit.

Also, changed the integration routine in the AIAFile object so that it saves
the last integral internally.
Fixed serious error in reference array

I made a serious mistake while generating the reference array for my GCMS
fitting. If masses for the reference spectra were below the lowest mass that
was being detected, they were wrapped around to the other end of the mass
spectrum, which meant that I had intensities at very high masses.

Added a couple of lines of code to fix that issue, and things seem to be
better now.
Some cleanup on calibration.py

Minor cleanup. No big changes to analysis code.