Refactor the software options dictionary to make it more user friendly

[tyronerees]

The current method of defining options is both complicated for the user and hard to maintain.

Options should be controlled in a single place so that setting an option is consistent, with priority:

1. Values set in the example script.
2. Values set in the options file.
3. Values set as a default programmatically.

Options should also be able to be set easily, and have clearly defined default values.

[tyronerees]

related to #231?

[AndrewLister-STFC]

This issue needs rewording as per our discussion last week

[AndrewLister-STFC]

I think switching from json to configparser (.ini) compatible files would be good.

It has less clutter (like the brackets in json), supports comments, and looks a bit more presentable.

In my first draft of this, I'll use config parser, but I can change it if people prefer json