[eluser]Colin Williams[/eluser]
User Guide, Mr. Lerner. Cover-to-cover. No stopping for a break.
And to expand on "inparo's" (when did first and last names become obsolete.. I digress) explanation, index.php is the default front controller for a single application. You could have a second application with tacosalad.php as its front controller. It allows for having multiple apps. I'm pretty sure this is how you'll be able to "drop" EE 2.0 on your existing CI installation, because it will just be an app folder and a front controller.