Merge add_metadata and filename_handling

`add_metadata` contains the changes necessary so `cosmicx` gets the readnoise and gain from the FITS header, if those parameters are to found there. `filename_handling` has just a couple changes so that the pipeline can accept `_flt.fits` files in addition to `_c0m.fits` files. 

`filename_handling` appears to run successfully (up to Astrodrizzle) on inputs from all six detectors.