Ah yes, luckily I am currently developing a flask application at the moment.
You are currently missing the static folder which by default flask looks into, a folder structure something like this:
|FlaskApp
----|FlaskApp
--------|templates
- html files are here
--------|static
- css and javascript files are here
Two important default folders that Flask will look into templates and static.
Once you got that sorted you use this to link up with your javascript files from your html page:
<script src="{{url_for('static', filename="somejavascriptfile.js")}}"></script>
Plus – A good article to read but not super related but it talks about the folder structure of flask is this: https://www.digitalocean.com/community/tutorials/how-to-deploy-a-flask-application-on-an-ubuntu-vps