How to create a initial_migrations from an existing schema

django_initial_migrations.md

Here are the steps (for whoever runs into this problem):

1. Empty the django_migrations: table: delete from django_migrations;
2. For every app, delete its migrations folder: rm -rf <app>/migrations/

   find . -path "*/migrations/*.py" -not -name "__init__.py" -delete
   find . -path "*/migrations/*.pyc"  -delete
   

3. Reset the migrations for the "built-in" apps: python manage.py migrate --fake
4. For each app run: python manage.py makemigrations <app>. Take care of dependencies (models with ForeignKey's should run after their parent model).
5. Finally: python manage.py migrate --fake-initial

After that I ran the last command without the --fake-initial flag, just to make sure.

Now everything works and I can use the migrations system normally.

Update for Django >= 1.9 users:

I had this scenario again with a Django 1.9.4, and step 5 failed. All we have to do is replace --fake-initial with --fake to make it work.