simpler docs (#921)

Improved the docs around v3 config to:

- Make it more obvious that many fields are now nested under `agent:`
- Remove fields which should not be included in `agent configurations`,
but are instead top level fields (eg. `version`)
- Simplfy examples
- Modify examples that include code snippets to explicitly nest relevant
fields under `agent`
- Remove the "full example config" and replace with various smaller
configuration examples.