I use this to create the basic app engine skeleton project for quick prototyping. Most of the setup can also be used for final production app, your files should be organized if you follow it's core setup.
Summary of things::
lib/ - will hold your custom libraries, thirdparty libraries usually just go on root folder
models/ - all your endpoint messages and datastore models here
services/ - web services like cloud endpoints or your custom jsonrpc services
mappers/ - model long tasks goes here for scripting or any task like actions
static/ - js/css/images and all other static files (templates for js html)
src/ - frontend code goes here including js and css
templates/ - jinja2 templates goes here
web/ - webpage handlers
tests/ - unit testing tests goes here
config.py - any configurable things on your project to easily edit later when you adjust things
routes.py - all your routing needs for your url mapping to webpage handlers
Note that this is just a guideline, following it will just make life things easier when your app grows to hundreds of files
# If you are using Homebrew in OSX
rm -rf ext_lib/* && echo -e "[install]\nprefix=" > ~/.pydistutils.cfg && pip install -t ext_lib -r requirements.txt && echo "" > ~/.pydistutils.cfg
# Regular python command
pip install -t ext_lib -r requirements.txt
# Frontend Dependencies and Watcher command
cd src
npm install
gulp watch