yaml config structure

Let's create a separate root section for the `doer-config.yaml` called `settings`.

This should include the sub-sections `api` and `app`, and we should distribute each setting and flag under its own section.
No configuration settings should be at root level. Thus, the general structure of the yaml file should be:

- app_name
- connections
- sources
- sql
- endpoints
- settings
- app
- api