Add nightly bias and bad column flagging into desi_run_night

[akremin]

Overview

This is the final PR in the effort to add the bias modeling and bad column identification into the pipeline. This pull request incorporates darks into the reprocessing code, desi_run_night.

Most of the underlying functions were updated yesterday. This primarily edits the coordination script desi_run_night so that it keeps and submits dark jobs. While doing so I also implemented a small feature that moves the calibrations to the start of the exposures so that cals are always processed first, in order of: 1) the first 300s dark, 2) arcs+flats, 3) science exposures.

I also fixed a bug meant to catch darks of the wrong EXPTIME.

Reprocessing Test

I've tested this on 20211020 with multiple darks and it runs the first dark and skips the subsequent darks as expected. I tested it on one "typical" night, 20211027, and it did the proper thing there as well. Finally I ran a test night of jobs, stopping halfway through the sciences. The dependencies in the queue were correctly set and the jobs ran properly. I verified that the biases were used and the badcolumn files were also used. This was night 20211026 in the test prod.

commands:
desi_run_night --dry-run-level=1 -n 20211020 &>test_reprocdarks_20211020.log &
desi_run_night -n 20211026
desi_run_night --dry-run-level=1 -n 20211027

The prod used for testing:
/global/cfs/cdirs/desi/users/kremin/spectro/redux/reprocdarks

daily processing (re-) Test

In addition, since I changed two thing in the daily processing script, I reran in dry-run mode:
desi_daily_proc_manager --override-night=20211020 --dry-run-level=1 --ignore-cori-node

and it once again did the right thing. The prod used for that test was:
/global/cfs/cdirs/desi/users/kremin/spectro/redux/usedarks

Note: I had already tested that night in the PR yesterday. Those results are in *.orig.csv versions of the output tables, while the standard names are the new ones produced for this test. I chose that night because it had two darks, which tests slightly more of the new coding logic.

[coveralls]

Coverage decreased (-0.01%) to 26.316% when pulling 0ef4d2d on nightlybias-reproc into 0327328 on master.

[sbailey]

Looks good, thanks. Merge when ready. I will trust your tests and the upcoming run to catch any remaining issues if any.