AWS documentation describes how you authenticate to Github using your browser, and that you're currently logged into Github as a valid user with permission to the repository you want to deploy from:
http://docs.aws.amazon.com/codedeploy/latest/userguide/github-integ.html#github-integ-behaviors-auth
Is there any way to setup CodeDeploy without linking my user and having a browser? I'd love to do this using webhooks on each repository and AWS API calls, but I'll make a Github 'service user' if I have to.
More examples: http://blogs.aws.amazon.com/application-management/post/Tx33XKAKURCCW83/Automatically-Deploy-from-GitHub-Using-AWS-CodeDeploy
I'd love to use webhooks on my repo, or set them up myself, than permit AWS access to every repository on my Github account.
There does not appear to be an alternative to doing the OAuth flow in your browser at this point. If you're concerned about opening your whole Github account up to Amazon, creating a service user is probably the best approach, unfortunately it seems this user still needs administrative access to your repos to set up the integration.