I'm not a Github expert so I'm not entirely sure. I know that you can make a new repo, download the old version of PFE you based on the project on, commit, then download the new version of PFE, and that will show you all of the changes. But I don't know if there's a way to go from that to adding all the changes to the project. Maybe if you use a separate branch for it and then merge the branch back into main.