Add migrations using alembic.

* #39 Add Flask-Migrate dep

* #39 Make it such that flask db init can run

https://github.com/miguelgrinberg/Flask-Migrate/issues/196#issuecomment-381343393

* Run flask db init, update migrations.env, commit artifacts

* Set up a script such that you can `docker-compose exec files bash -c 'cd /service; FLASK_APP="files/cli:app" flask '` and have it do whatever flask thing you want

* Fix circular dependency

* import * is evil

* Initial alembic migration, has issues with constraints and nullable columns

* Bring alts table up to date with alembic autogenerate

* Rerun flask db revision autogenerate

* Bring award_relationships table up to date with alembic autogenerate

* [#39/alembic] files/classes/__init__.py is evil but is at least explicitly evil now

* #39 fix model in files/classes/badges.py

* #39 fix model in files/classes/domains.py and files/classes/clients.py

* #39 fix models: comment saves, comment flags

* #39 fix models: comments

* Few more imports

* #39 columns that are not nullable should be flagged as not nullable

* #39 Add missing indexes to model defs

* [#39] add missing unique constraints to model defs

* [#39] Temporarily undo any model changes which cause the sqlalchemy model to be out of sync with the actual dump

* #39 Deforeignkeyify the correct column to make alembic happy

* #39 flask db revision --autogenerate now creates an empty migration

* #39 Migration format such that files are listed in creation order

* #39 Better first revision

* #39 Revert the model changes that were required to get to zero differences between db revision --autogenerate and the existing schema

* #39 The first real migration

* #39 Ensure that foreign key constraints are named in migration

* #39 Alembic migrations for FK constraints, column defs

* [#39] Run DB migrations before starting tests

* [#39] New test to ensure migrations are up to date

* [#39] More descriptive test failure message

* Add -T flag to docker-compose exec

* [#39] Run alembic migrations when starting the container

migrations/README

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+Single-database configuration for Flask.

migrations/alembic.ini

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+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d_%%(minute).2d_%%(second).2d_%%(rev)s_%%(slug)s
+timezone = UTC
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

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+from __future__ import with_statement
+
+from files.classes import *
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+connection_string = current_app.config.get('DATABASE_URL')
+
+config = context.config
+config.set_main_option('sqlalchemy.url', connection_string)
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+from files.__main__ import Base
+target_metadata = Base.metadata
+
+config.set_main_option(
+    'sqlalchemy.url',
+    str(current_app.extensions['migrate'].db.get_engine().url).replace(
+        '%', '%%'))
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=target_metadata, literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    connectable = current_app.extensions['migrate'].db.get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            process_revision_directives=process_revision_directives,
+            **current_app.extensions['migrate'].configure_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

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+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

migrations/versions/2022_05_12_02_54_34_0aef77162269_create_empty_first_revision.py

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+"""create empty first revision
+
+Revision ID: 0aef77162269
+Revises: 
+Create Date: 2022-05-12 02:54:34.564536+00:00
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '0aef77162269'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###

migrations/versions/2022_05_12_03_08_32_4a1f7859151b_update_db_to_match_models_at_fork_time.py

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+"""update db to match models at fork time
+
+Revision ID: 4a1f7859151b
+Revises: 0aef77162269
+Create Date: 2022-05-12 03:08:32.417479+00:00
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '4a1f7859151b'
+down_revision = '0aef77162269'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('submissions', sa.Column('bump_utc', sa.Integer(), server_default=sa.schema.FetchedValue(), nullable=True))
+    op.create_foreign_key('comments_app_id_fkey', 'comments', 'oauth_apps', ['app_id'], ['id'])
+    op.create_foreign_key('commentvotes_app_id_fkey', 'commentvotes', 'oauth_apps', ['app_id'], ['id'])
+    op.create_foreign_key('modactions_user_id_fkey', 'modactions', 'users', ['user_id'], ['id'])
+    op.create_foreign_key('submissions_app_id_fkey', 'submissions', 'oauth_apps', ['app_id'], ['id'])
+    op.create_foreign_key('votes_app_id_fkey', 'votes', 'oauth_apps', ['app_id'], ['id'])
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint('votes_app_id_fkey', 'votes', type_='foreignkey')
+    op.drop_constraint('submissions_app_id_fkey', 'submissions', type_='foreignkey')
+    op.drop_constraint('modactions_user_id_fkey', 'modactions', type_='foreignkey')
+    op.drop_constraint('commentvotes_app_id_fkey', 'commentvotes', type_='foreignkey')
+    op.drop_constraint('comments_app_id_fkey', 'comments', type_='foreignkey')
+    op.drop_column('submissions', 'bump_utc')
+    # ### end Alembic commands ###

migrations/versions/2022_05_16_19_42_28_16d6335dd9a3_add_usernotes_constraints.py

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+"""add usernotes constraints
+
+Revision ID: 16d6335dd9a3
+Revises: 4a1f7859151b
+Create Date: 2022-05-16 19:42:28.708577+00:00
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '16d6335dd9a3'
+down_revision = '4a1f7859151b'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('usernotes', 'note',
+               existing_type=sa.VARCHAR(length=10000),
+               nullable=False)
+    op.alter_column('usernotes', 'tag',
+               existing_type=sa.VARCHAR(length=10),
+               nullable=False)
+    op.create_foreign_key('usernotes_author_id_fkey', 'usernotes', 'users', ['author_id'], ['id'])
+    op.create_foreign_key('usernotes_reference_comment_fkey', 'usernotes', 'comments', ['reference_comment'], ['id'], ondelete='SET NULL')
+    op.create_foreign_key('usernotes_reference_post_fkey', 'usernotes', 'submissions', ['reference_post'], ['id'], ondelete='SET NULL')
+    op.create_foreign_key('usernotes_reference_user_fkey', 'usernotes', 'users', ['reference_user'], ['id'], ondelete='CASCADE')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint('usernotes_reference_user_fkey', 'usernotes', type_='foreignkey')
+    op.drop_constraint('usernotes_reference_post_fkey', 'usernotes', type_='foreignkey')
+    op.drop_constraint('usernotes_reference_comment_fkey', 'usernotes', type_='foreignkey')
+    op.drop_constraint('usernotes_author_id_fkey', 'usernotes', type_='foreignkey')
+    op.alter_column('usernotes', 'tag',
+               existing_type=sa.VARCHAR(length=10),
+               nullable=True)
+    op.alter_column('usernotes', 'note',
+               existing_type=sa.VARCHAR(length=10000),
+               nullable=True)
+    # ### end Alembic commands ###