Upgrading CI3 under version control

I have a project that runs locally and on a live server under version control (git). I want to do a CI update by replacing all content in the system folder with newer CI version content. Is this list the correct way to do it, on my local machine:

1. Empty system folder
   
2. Commit
   
3. Paste in new content to the system folder
   
4. Commit
   
5. Push to GitHub and live server
   

Or does version control understand that all files are replaced, so I don't have to commit in step 2?