chore: port remaining in-lined scripts to scripts/

[a-frantz]

Describe the problem or feature in addition to a link to the issues.

Fixes #214

Also adds a new Docker convention that scripts copied from scripts/ should use the same path within the image (e.g. scripts/star/sort_star_input.py should be copied to and called as /scripts/star/sort_star_input.py)

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