Prevent sync deploying from git on shared hosting?

Hello :wave: I’m pretty green, so bear with me :sweat_smile:

Hostinger allows deployment directly from a git repo, but the install path of the deployment has to be completely empty for it to work so…

In the repo I am developing out of (using create react app), I had the idea to add my fork of Cockpit as a submodule to the public directory so that it is included in the build → and then I can commit to a separate repo from the created build directory and deploy through Hostinger from there.

I understand I need to prevent my config and storage directories from being modified on the production.

My concern is how this works when deploying direct from git. If I make frontend changes then build and commit, how do I prevent the config and storage folders from syncing to the repo? Is this possible?

Another option I thought about was deploying the frontend into a subdirectory rather than the document root and using .htaccess to redirect, while keeping the Cockpit installation in the root, but that seems kind of beat-around-the-bush-ey.