Remove flask-script, move commands to click

click (http://click.pocoo.org/) is used by flask to run its cli args.
In removing flask_script (it's unmaintained), we had to migrate all our
commands to use click. This is a change for the better in my eyes - you
don't need to define the command in several places, and it makes
managing options a bit easier.

View diff with whitespace turned off unless you're a masochist.

scripts/run_app.sh

@@ -3,4 +3,4 @@
 set -e
 
 source environment.sh
-python3 application.py runserver
+flask run -p 6011