How can I remove all files in my git repo and update/push from my local git repo?

You could do it like this:

cd /tmp
git clone /your/local/rep  # make a temp copy
cd rep
git rm -r *                # delete everything
cp -r /your/local/rep/* .  # get only the files you want
git add *                  # add them again
git status                 # everything but those copied will be removed
git commit -a -m 'deleting stuff'
cd /your/local/rep
git pull /tmp/rep          # now everything else has been removed

There's probably a oneliner for that…

First, remove all files from your Git repository using: git rm -r *

After that you should commit: using git commit -m "your comment"

After that you push using: git push (that's update the origin repository)

To verify your status using: git status

After that you can copy all your local files in the local Git folder, and you add them to the Git repository using: git add -A

You commit (git commit -m "your comment" and you push (git push)