Related to the first point, I think it might be appropriate to establish a convention for the file in which to use Commanded.Application. The current Application documentation uses MyApp.Application, but almost every Elixir application already has such a file that configures it's OTP application.

Some real-world examples are Bonfire uses Bonfire.EventApp and @vasspilka's Bank example creates a Bank.Core namespace with the Commanded application at Bank.Core.Application.

As a brand new user, this was definitely something that confused me. Upvote for some clarifying "best practice" documentation about how to structure Commanded Applications in both fresh projects (ala mix new --sup) and within phoenix projects.