If you are on Linux:
git fetch
for file in `git diff origin/master..HEAD --name-only`; do rm -f "$file"; done
git pull
The for loop will delete all tracked files which are changed in the local repo, so git pull
will work without any problems.
The nicest thing about this is that only the tracked files will be overwritten by the files in the repo, all other files will be left untouched.