I try different commands and some of the answers help me. Only this sequence in my case fixed both broken dependencies in migrations in MYAPP and clean all past migrations starting from scratch.

Before doing this ensure that database is already synced (e.g. do not add a new Model field here or change Meta options).

rm -Rf MYAPP/migrations/*
python manage.py makemigrations --empty MYAPP
python manage.py makemigrations
python manage.py migrate --fake MYAPP 0002
Where 0002 is the migration number returned by the last makemigrations command.

Now you can run makemigrations / migrate again normally because migration 0002 is stored but not reflected in the already-synced database.

if you really want to go crazy delete all the tables in teh database related to the app and then

DELETE FROM django_migrations WHERE app='registry'



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this is what I do

first I clear out everything:

rm -Rf appname/migrations

fab database.drop_all
fab database.init
fab django.manage:migrate
fab django.manage:syncdb


then I re-add the app

fab django.manage:"makemigrations appname"
fab django.manage:migrate


at that point I have working table
so again

rm -Rf {ON HOST}/appname/migrations
fab ONHOST database.drop_all
fab ONHOST database.init
fab ONHOST deploy.sync    <--- CRITICAL STEP DO NOT FORGET
fab ONHOST django.manage:migrate
fab ONHOST django.manage:syncdb