The apps are in nested modules. I personally prefer this approach too, since it makes it clear what imports belong to the project.
See this long forum discussion on apps: Why do we need apps?
Can’t say I know anything about Misago, but I like starting with the URLconf to get a grip on a new project: https://github.com/rafalp/Misago/blob/master/misago/urls.py
Hope that helps!