Expert needed for PHP GiTHub Repository issue

Hello We use PHP/CI as our development platform and all our code is stored in a GitHub repository. Our Development work is updated on a Weblink (called from AWS Storage) where we show the Application Product to all our customers, and once any Customer agrees to buy our product, we take a Pull from GitHub and set up the same Folder with all the files in AWS Server space so that Customer can get a link to their new Application. In almost every case, the Customer who has purchased the application also asks us about some customization in the application. When we start the customization, we work on localhost and push it to the original repository, and after finishing the customization work, we take a pull and upload the same application folder on the customer application folder. Problem Statement: The customization is customer specific and we tend to change the code in the main repository, and every time a new customer gives us the requirement, we need to revert the code back to where it was before we started the customization. We need help from PHP/Github expert who can advise how to make customer-specific changes so that we don't end up doing modifications in our main application every now and then and keep reverting to the old code which needs to be given to lots of customers. The project is an advisory basis and if the solution suggested by the freelancer works, we can pay a flat amount on the same day.