I just deleted ALL the code from a file in my project and committed the change to my local git (on purpose). I did
git pull upstream mas
Just a friendly reminder if you have files locally that aren't in github and yet your git status
says
Your branch is up to date with 'origin/master'. nothing to commit, working tree clean
It can happen if the files are in .gitignore
Try running
cat .gitignore
and seeing if these files show up there. That would explain why git doesn't want to move them to the remote.