Versioning an already live laravel application with GIT

I have a live laravel site working and running on a VPS. Currently the application is running on a subdomain for testing. The site is not versioned and I would like to use GIT to version it, then pull the changes to my Homestead Dev environment.

The current app is in ~/repos/site whilst the laravel public folder is in the public_html folder. I would like to initialise the actual site.git inside ~/repos/git-repos whilst maintaining the ~/repos/site folder as this is being used to run the app.

How do I achieve this? Because it is live I am concerned it could break the app. I think I need to run git init however the folder is not bare so I am not sure as I have only ever used GIT using --bare flag, using git clone to the live server from my dev environment then GIT pushing the changes.

EDIT:

I guess the complication is that the public_html folder, because it holds the assets for the front-end site, needs to be versioned also, but is in a different folder. Can GIT do this?

Thank you for your help in advance

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