what's in a node.js elastic beanstalk zip file and how do I get it to run a script on deploy?

Should the zip file of my application include the node_modules folder? Should I be zipping up a top-level folder that contains all my application files or should I not include the top root folder like the instructions for amazon lambda?

Do I have to set the web application port to an environment variable like in heroku? Does the app start by calling npm start and looking at the package.json or do I have to have a file called server.js like in opsworks?

How can I have it run a small migration script before it starts - can I just put that in npm start?

Can I get it to run npm install on deployment rather than copying over the node_modules folders?