If the file is indeed in your root directory, then the link (http://mydomain.com/breakfastmenu.pdf) should work. In my opinion uploading files in the WordPress media manager is best, since you can copy/paste the url directly. That way you always know for sure the url works. I hope that makes any sense 😉
If you only insert a link to the filename, then the server will look for that file in the current page. That’s why using a complete url is best.