eCommerce platform software architecture

I've an eCommerce platform building using Laravel, MySQL and jQuery. It's working good and if anyone become interested, I just deploy the entire source cod e in environment / Hosting. This is not a good model of course. Because everyone ask for small or large amount of change and I had to do this. Imagine when there will be 100 separate deploy and I had to manage 100 separate source. So How do I make my system architecture so that I'll have a core / base source code. To make any any change / update on specific deployment, it will be theme / plugin / extension based . Also if I introduce an API layer then I could handle the Web, Mobile App and POS as well ? Is the API should be part of source code or a individual single API and all the deployment will use that API ?