I have a working sample site with the file system as such (https://github.com/alvations/APE):
APE
\app
\templates
base.html
index.html
instance.html
__init__.py
hamlet.py
config.py
run.py
I have created a flask project on https://www.pythonanywhere.com and the file system is as such:
/home/alvations/
/Dropbox/
/mysite/
/templates
base.html
index.html
instance.html
flask_app.py
/web2py/

Where do I place my run.py in my pythonanywhere project?
How do I use the same file structure as my the project in my Github on pythonanywhere?