Then from your description (I assume you’re using some GUI) the remote will always be out of sync with your local, because it will have files in a structure that is different to what it actually is. I think you’re misunderstanding what GitHub is: it’s not just a place to store files. It’s a record of files and the changes made to them, and it’s the same on whichever computer you view it on. The file structure on your computer will be the same as it is on GitHub because it’s the same thing. Repos which have a server folder and a client folder aren’t doing anything special: their project folder just has two folders in it.
I think what you’ve done is tried to make a repo out of either the server or client folder, rather than the folder that they live in. You can’t then have anything outside of there as part of the repo
In what folder in your project is the
.git folder? That’s the thing that makes git work, the thing that contains a record of your files and the changes to them. If it’s not in the root folder, delete it and reinitialise git in the project root, because it’s in the wrong place.