GitSync - adds pages folder to root

Hey everyone,
I try to set up the GitSync plugin, but everytime I connect it an issue occurs:
The GitSync plugin pushes to Github and creates a pages folder in the root.

Screenshot- Notice the commit message: (Grav GitSync) Automatic Commit from tilb

When I check if the GitSync plugin has added the pages folder to production as well, I am surprised: as you can see, in production the pages folder is not to be found in root.

Folders in root in production

So I sync Github and pull the pages folder as commited by the GitSync plugin. Now I'd like to see if I can do any change in development and sync it to check if the webhook does anything. Now, to my surprise, a pages/system folder is automatically added, as you can see below:

A system folder is automatically added to the pages folder

What is the issue here? Can I do anything about it, or is it a GitSync bug?

You cannot use a full Grav instance as repository linked to GitSync, it has to follow the same structure of a Skeleton, just the user folder.

Checkout the videos in https://github.com/trilbymedia/grav-plugin-git-sync#videos-setup-and-demo