Convert Autocorpus class methods to functions

[AdrianDAlessandro]

The Autocorpus class can remain as a class, however most of the methods it currently has are better suited to being standalone functions.

The most useful functionality that should remain in the class is related to the outputs. It behaves most like a data class, so there's an argument to convert it to a data class.

Edit: Output processing is done in run.py. This should probably be adjusted with this refactor

[alexdewar]

@AdrianDAlessandro Not sure if you deliberately left this issue out of this iteration because it's high level/more complicated than the others or by mistake... We could stick it in the next iteration and mark it as on hold, if so.

[AdrianDAlessandro]

No, that was an accident. I will put it in and we can discuss on Tuesday