Assorted cleanup of xfel-calibrate

Description

Now that @roscar has added some tests for the CLI, I though I'd start cleaning up the code a bit. This is a combination of various minor changes, which I'll describe inline.

How Has This Been Tested?

Run xfel-calibrate from my account on Maxwell, checked that output files, report, details from Slurm are still produced in the output folder as before.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• Refactor (refactoring code with no functionality changes)

Checklist:

• My code follows the code style of this project.

Reviewers

@roscar @ahmedk