I don't really think it's the Custom model that's at fault here - this migration was created months ago. The point is that auth migrations are stored in, to my mind, the wrong place (in /Users/XXXX/.virtualenvs/YYYY/lib/python2.7/site-packages/django/contrib/auth/) and a separate problem revealed this to me. I've included a stack trace below though.
Running migrations:
Applying auth.0002_customer_payingcustomer_projectmanager_staff...Traceback (most recent call last):
File "./manage.py", line 10, in <module>
execute_from_command_line(sys.argv)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/core/management/__init__.py", line 385, in execute_from_command_line
utility.execute()
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/core/management/__init__.py", line 377, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/core/management/base.py", line 288, in run_from_argv
self.execute(*args, **options.__dict__)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/core/management/base.py", line 338, in execute
output = self.handle(*args, **options)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/core/management/commands/migrate.py", line 160, in handle
executor.migrate(targets, plan, fake=options.get("fake", False))
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/migrations/executor.py", line 63, in migrate
self.apply_migration(migration, fake=fake)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/migrations/executor.py", line 91, in apply_migration
if self.detect_soft_applied(migration):
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/migrations/executor.py", line 135, in detect_soft_applied
apps = project_state.render()
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/migrations/state.py", line 67, in render
model.render(self.apps)
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/migrations/state.py", line 311, in render
body,
File "/Users/XXXX/.virtualenvs/gu_portal/lib/python2.7/site-packages/django/db/models/base.py", line 155, in __new__
raise TypeError("%s cannot proxy the swapped model '%s'." % (name, base_meta.swapped))
TypeError: PayingCustomer cannot proxy the swapped model 'emailcustomuser.User'.