Refactor scripts to simplify code base as much as possible

[adamltyson]

No description provided.

[viktorpm]

Loading annotations and references should be independent of mesh generation

[willGraham01]

Also going to bump this - most of the atlas generation scripts themselves follow the same pattern: get template, structure heirachy, wrap up. In the majority of cases these are identical save for the input data and file paths, etc.

It wouldn't be unfeasible to create an atlas generation base class, rather than a folder of scripts (or at least, a set of general purpose functions).

Then this repeated, general functionality can go in the base class/functions, and atlases can be added either as instances (setting appropriate class member values like file location, etc) or a derived class (in the event that certain steps genuinely need to be edited from the standard workflow).