How to multiple files on server with github repository?

Question

git

Good afternoon.
There is a repository on github with the source of the site. There is also a vps where the site is configured. On the server in the root folder of the site there are several files that are not in the repository.
How can I update only the css and templates folders, and leave the rest of the folders / files in the project?
Or how to update only the files that are in the repository, and those that are not, do not touch in the root folder of the project on the server.
git clone "repo" fails if the folder already exists and is not empty. Or am I doing something wrong)

Answer 1

You clone into an empty folder and then transfer its contents to the site folder along with the .git folder.
You add unnecessary files to .gitignore.