GitHub push to AWS Elastic Beanstalk

Have you considered using sources via .ebextensions with your shared files stored in S3?

http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/customize-containers-ec2.html

I have used sources to deploy shared files (sitemaps) that are built by our app server (and stored in S3).

sources: 
  "c:/inetpub/sitemaps": http://[S3 bucket]/sitemaps.zip

container_commands:
  01-copy-sitemaps-to-www:
    command: copy c:\\inetpub\\sitemaps\\*.* c:\\inetpub\\wwwroot\\ > copy_sitemaps_to_www.log 2>&1
    waitAfterCompletion: 5

• If you don't have too many submodules (and you're not changing or updating them often) you could just replace them with the static files instead.

• Many people in the PHP community are starting to move away from managing dependencies with Git submodules to using Composer http://getcomposer.org/. This might make part of your deployment flow simpler.

• There is also a solution outlined here https://forums.aws.amazon.com/message.jspa?messageID=474880 The last comment (Aug 1, 2013 1:37 PM by oquismail) shows you how to modify Elastic beanstalk configuration files

• You could consider managing deployments through https://github.com/briandilley/ebs-deploy (Python based command line tools for managing Amazon Elastic Beanstalk applications.)