Local development and deploying from same repo

I have Discourse running locally based off of this. No problems, worked fine. Beginners Guide to Install Discourse on macOS for Development
I am getting ready to deploy Discourse to a production environment using Docker via Digital Ocean (Recommended in many places)
My question is if I deploy Discourse via GitHub - discourse/discourse_docker: A Docker image for Discourse as recommended how do I make changes to my local installation and get them deployed to production?

The question itself implies something bad is happening.

Customizations should be done through plugins and Admin, Customize, not by modifying core Discourse code.