Each call of makemigrations creates a migration for custom user account.

[efrinut@…]

DJANGO_APPS = (
    'django.contrib.contenttypes',
    #'django.contrib.admin',

    'django.contrib.auth',
    'django.contrib.sessions',
    'django.contrib.sites',
    'django.contrib.messages',
    'django.contrib.staticfiles',
    'django.contrib.admindocs',
    'django.contrib.humanize',
    'django.contrib.sitemaps',
    'django.contrib.flatpages',
)

EXTERNAL_APPS = (
    'haystack',
    'storages',
    'pipeline',
    'endless_pagination',
    'easy_thumbnails',
    'mptt',
    'rest_framework',
    'crispy_forms',
    'crispy_forms_foundation',
    'taggit',
)


SITE_APPS = (
    'accounts',
    # 'core',
    # 'images',
    # 'streams',
    # 'links',
    # 'entries',
)

INSTALLED_APPS = DJANGO_APPS + EXTERNAL_APPS + SITE_APPS

AUTH_USER_MODEL = 'accounts.User'

models.py:

from django.db import models
from django.contrib.auth.models import AbstractUser
from django.core.urlresolvers import reverse


class User(AbstractUser):
    description = models.TextField(null=True, blank=True, verbose_name=u"Write something about yourself")
    link_blank = models.BooleanField(default=False, verbose_name=u"Open links in new window")
    link_direct = models.BooleanField(default=False, verbose_name=u"Skip directly to the link")

    class Meta:
        db_table = 'auth_user'

    def get_absolute_url(self):
        return reverse("user:detail", kwargs={'pk': self.pk})

    def get_edit_url(self):
        return reverse("user:edit", kwargs={'pk': self.pk})

migrations:

0001_initial
0002_auto_20140502_1656
0003_auto_20140502_1703
0004_auto_20140502_1703

0001_initial

# encoding: utf8
from __future__ import unicode_literals

from django.db import models, migrations
import django.utils.timezone
import django.core.validators


class Migration(migrations.Migration):

    dependencies = [
        (b'auth', b'__first__'),
    ]

    operations = [
        migrations.CreateModel(
            name=b'User',
            fields=[
                ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
                (b'password', models.CharField(max_length=128, verbose_name='password')),
                (b'last_login', models.DateTimeField(default=django.utils.timezone.now, verbose_name='last login')),
                (b'is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
                (b'username', models.CharField(help_text='Required. 30 characters or fewer. Letters, digits and @/./+/-/_ only.', unique=True, max_length=30, verbose_name='username', validators=[django.core.validators.RegexValidator('^[\\w.@+-]+$', 'Enter a valid username.', 'invalid')])),
                (b'first_name', models.CharField(max_length=30, verbose_name='first name', blank=True)),
                (b'last_name', models.CharField(max_length=30, verbose_name='last name', blank=True)),
                (b'email', models.EmailField(max_length=75, verbose_name='email address', blank=True)),
                (b'is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
                (b'is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
                (b'date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
                (b'description', models.TextField(null=True, verbose_name='Write something about yourself', blank=True)),
                (b'link_blank', models.BooleanField(default=False, verbose_name='Open links in new window')),
                (b'link_direct', models.BooleanField(default=False, verbose_name='Skip directly to the link')),
                (b'groups', models.ManyToManyField(to=b'auth.Group', verbose_name='groups', blank=True)),
                (b'user_permissions', models.ManyToManyField(to=b'auth.Permission', verbose_name='user permissions', blank=True)),
            ],
            options={
                'abstract': False,
                'verbose_name': 'user',
                'verbose_name_plural': 'users',
            },
            bases=(models.Model,),
        ),
    ]

0002_auto_20140502_1656 - 0004_auto_20140502_1703

# encoding: utf8
from __future__ import unicode_literals

from django.db import models, migrations
import django.core.validators


class Migration(migrations.Migration):

    dependencies = [
        (b'accounts', b'0001_initial'),
    ]

    operations = [
        migrations.AlterField(
            model_name=b'user',
            name=b'username',
            field=models.CharField(help_text='Required. 30 characters or fewer. Letters, digits and @/./+/-/_ only.', unique=True, max_length=30, verbose_name='username', validators=[django.core.validators.RegexValidator('^[\\w.@+-]+$', 'Enter a valid username.', 'invalid')]),
        ),
    ]

Each migration applies correctly but it does not change anything when you enter manage.py makemigrations.

[Tim Graham]

You are using the latest master? This was reported in #21638 but subsequently fixed.

[anonymous]

Yeah,

I did uninstall django and installed it by

 pip install git+https://github.com/django/django@stable/1.7.x

[Tim Graham]

Could you try again? I can't reproduce this issue with the model you provided:

$ python manage.py makemigrations accounts
No changes detected in app 'accounts'

The initial migration that was generated for me only has

options={
    'db_table': 'auth_user',
},

[Tim Graham]

#22588 could be related.