[Django]-Django: manage.py custom command not found

I had the same exact problem. After a few hours of searching through manage.py code it showed up that this was caused by my settings file configurations. I was using Mezzanine as my CMS. When you use it Mezzanine kind of says that you can put some apps under OPTIONAL_APPS variable, so I had my custom app under this variable but not in INSTALLED_APPS. Moved back to INSTALLED_APPS and everything started working as expected.

Make sure you have your application nowhere else than under INSTALLED_APPS. manage.py looks exactly to this constant.