Move away content from public_html in a git repo on live server

In your local dev machine you create a public (or public_html) folder. Move everything in there. Push it to GitHub and after running git on your public server you will need to change document_root to your new public folder.

Or scrap git on live server and re-download everything, if you don't want double public_html folders.

OK, so how about if I change my project on my local machine to something like this (and change the folder paths in index.php accordingly):

my_project
 l--public_html/
 l   l--index.php
 l--application/
 l--views/
 l--system/

Finally, I push to my live server one level up (from the folder  public_html).