I use this script to sync my fork with the upstream (original repo).

git-update.sh

#!/bin/sh

# fetches the new stuff from upstream. I hope you've added the link to the original repo as 'upstream' 
git fetch upstream 
git checkout master 

# prunes unwanted branches
git fetch --all --prune

# merges without your master
git merge upstream/master 

#pushes it up to your fork.
git push