I have an AWS Elastic Beanstalk app, which I would like to customize — but beyond what the EB configuration (console) editing feature allows.

For example, I would like to specify exactly which Security Groups are applied to the EC2 instances and the Load Balancer (among other things).

I thought I could do this by editing the Cloudformation template associated with the EB environment, but I discovered that EB will overwrite my changes in some cases (e.g., when I make some change via the EB console).

Is there a way that I can make my Cloudformation changes permanent? I have seen some references to .ebextensions, but I need to have different configs for my different environments.

Are there other options?