As others have pointed out one could just delete all the files in the repo and then check them out. I prefer this method and it can be done with the code below
git ls-files -z | xargs -0 rm
git checkout -- .
or one line
git ls-files -z | xargs -0 rm ; git checkout -- .
I use it all the time and haven't found any down sides yet!
For some further explanation, the -z appends a null character onto the end of each entry output by ls-files, and the -0 tells xargs to delimit the output it was receiving by those null characters.