Configuration feature extras (#700)

Configuration feature extras (#700)

* [configuration] as top-level table in manifests

[config_vars] and [config_settings] are now [configuration.variables] and
[configuration.settings]

* Replace stderr warnings with regular ones

* Fix YAML output

* Rename `configuration.settings` to `@.values`

This is under the rationale that `settings` makes more sense for configuring
how Alire deals with the configuration.

* Update documentation for new config tables

* Fix obsolete comment