Adding A Moodle Project to Source Control

I'm not a php nor moodle developer. I worked as a python developer for many years and now work as a devops eng. One of my clients uses the moodle framework for their site with no source control. I've spoken with their lead developer and he insists there's no way to have a moodle repo without the entire directory structure in the repository, that is all the `auth`, `admin`, `backup`, `badges`, etc directories, since many files in those directories have been touched by their development team I did a file count and it's over 50K files, which is insane for a code repo. Has anyone managed to solve this problem for a moodle site before? Specifically a clean CI process using source control?