I think alan means "outside" of your web directory.
Like, when you log into the root of your server, you may see directories like:
mail
tmp
public
Then, when you go into the, "public" directory, there is all your php and html files for your website.
Well, the "root" where you have just those mail directories: "mail," "tmp," and, "public" would be a safer place to put your secret file.