Redo configuration entirely to better organize features

[zachbr]

The current configuration format has some organizational issues. To fix them as extensively as I'd like, there will need to be some breaking changes made to its format.

Because this is not an API, we will treat this as "breaking" and will need to make this a 2.0.0 level change. Migration may be possible and considered.

Generally the purpose of this change is to allow much more extensive customization of features and how they apply to all sides of the bridge.