modified to create superbias and move superbias to reffiles folder
-Added code to clear out herringbone correction folders before starting a new run
-Added code to copy the superbiases and superdarks to the reffiles folder
-started code to determine and update the best dark and bias reference files for a given observation
-Added code to time the reference file creation code
fixed minor bug in cleaning herringbone directory
Modified build_inventory to only rebuild files created during current run.
First test of terminating hung autofilet appears to have worked

Previously, build_inventory looked at the whole autofilet.log file. However
when multiple runs were performed, the code crashed when it created warning
arrays used the files in PSUB but then filled them with all of the files
in the log file including files from previous runs. It now only looks at
files in the log file after the most recent run. This could be an issue if
someone runs part way through ORIG, then stops, and then restarts, but the
code will print a warning that the number of files in PSUB does not match
the number of files being rebuild.
if code hangs on a set of xord, yord, it will try other combinations listed in AAS_README and exit if none of them work
fixed bug in line 701 which tried to write to the wrong fileunit
Edited to fix bugs and run pipeline end to end
Moved imports to the top of the program so I could run individual functions interactively
Code now writes how long it took to run each step
Added more options to the call to separate_obs to move flc files and copy not mv files to directory to create reference files
Added function make_reffiles instead of calling the make_reffiles function in REFSTIS_wrapper. This was enabled by a
refactor of the make_reffiles in REFSTIS_wrapper. It gives more flexibility in the options called to make each reference file type.
Added functionality to assign the appropriate reference file to an observation
Calstis and basic2D now write the trailer to log files
The code removed calibration products before running basic2d
Code now runs calibration pipeline with CTE correction in the middle