As a beginner, I finally noticed the issue with making changes to the live server I've been working on, now that I have a couple users on it, since I bring it down so often.

I created an EC2 image of my live server and set up a separate instance on EC2, so now I have 2 EC2 instances, Stage and Production. I set up GitHub and push changes to stage and test my code there, and when it's all done and working, I push it to the production branch, and everything is good. And there is a slight issue here since I name my files config_stage.js and config_production.js and set up .gitignore on each server, and in my code, I would have it read the ENV flags and set up the appropriate configs, is this the correct approach?

And my main question is: how do you keep track of non-code changes to the server? For example, I installed HAProxy, Stunnel, Redis, MongoDB and several other things onto the Stage server for testing and now that it's all working and good, how do I deploy them to production? Right now, I'm just keeping track of everything I installed and copying configuration files over, which is very tedious and I'm afraid I may have missed a step somewhere.

Is there a better way to port these changes over from my test server to my live server?