This adds a warning to xfel-calibrate if the chosen configuration may cause the result not be reproducible by xfel_calibrate.repeat, currently based on the presence of argument line flags. The user is forced to confirm this by pressing ENTER except when the additional --not-reproducible flag is passed. In the future, we may also use the latter flag to disable other checks or work only relevant for reproducibility.
Also, there's a new flag --skip-env-freeze to skip the pip freeze stage, which obviously breaks reproducibility.
Most important question and the reason I tag @calibration: Do you think the wording is good enough?
Extensive testing of the HED fast path.