I have few issues with this:

https://github.com/lincolnloop/django-layout

This structure leaves manage.py in the root path. Which mean other dirs will pollute this area, like run/, deploy/, log/, config/, lib/, bin/, cronjobs/, etc. You dirs woud stack to a long list.

I would suggest something like this:

    root/
      src/
        manage.py
      lib/
      run/
      docs/
      config/