Copy calibration_metadata.yml file to output directory instead of symlinking

Description

This is a follow-on to !661 (merged). Apparently symlinks in proc are undesirable, so this makes copies of calibration_metadata.yml instead.

How Has This Been Tested?

I ran:

xfel-calibrate agipd CORRECT --slurm-mem 700 --slurm-name correct_MID_agipd_202201_p002834_r60 \
   --cal-db-timeout 300000 --cal-db-interface 'tcp://max-exfl016:8015#8044' \
   --ctrl-source-template '{}/MDL/FPGA_COMP' \
   --karabo-da AGIPD00 AGIPD01 AGIPD02 AGIPD03 AGIPD04 AGIPD05 AGIPD06 AGIPD07 AGIPD08 AGIPD09 AGIPD10 AGIPD11 AGIPD12 AGIPD13 AGIPD14 AGIPD15 \
   --karabo-id-control MID_EXP_AGIPD1M1 --receiver-template '{}CH0' --adjust-mg-baseline \
   --bias-voltage 300 --blc-set-min --blc-stripes --cm-dark-fraction 0.15 \
   --cm-dark-range -30 30 --cm-n-itr 4 --common-mode --ff-gain 1.0 \
   --force-hg-if-below --force-mg-if-below --hg-hard-threshold 1000 \
   --low-medium-gap --mg-hard-threshold 1000 --overwrite --rel-gain \
   --sequences-per-node 1 --slopes-ff-from-files '' --xray-gain \
   --karabo-id MID_DET_AGIPD1M-1 \
   --in-folder /gpfs/exfel/exp/MID/202201/p002834/raw  --run 60 \
   --out-folder /gpfs/exfel/data/scratch/kluyvert/agipd-calib-2834-60-mddir

Output in /gpfs/exfel/data/scratch/kluyvert/agipd-calib-2834-60-mddir looks as I expect.

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist:

• My code follows the code style of this project.

Reviewers

@schmidtp @ahmedk