Where does AWS Elastic Beanstalk store application files?

I've spent the day reading up on AWS Elastic Beanstalk but as an AWS newbie there are still a few issues that I'm not clear on. As far as I can tell it would allow my PHP application to scale based on rules that I've set. I could have my database data stored on an Amazon RDS instance and my media storage on an Amazon S3 instance. As the site gained more traffic the system would add on new Amazon EC2 instances which would increase the compute capacity. But where are the PHP application files stored?

You upload them in ZIP format to an S3 bucket and Elastic Beanstalk takes them from there.