[URL rewrite] How to change base URI from index.php to domain root?

I had posted this comment regarding trying to change my site's base URI from andrewprokos.com/index.php--->to andrewprokos.com/:

http://gallery.menalto.com/node/55058

Valiant repsonded that I would need to hack the rewrite module to do that. Does anyone know how to do that? The reason I want to do this is so that the search engines will see my domain name and index page as one. All of the links coming into my site are pointing to the domain name, not the index page. I have an apache mod rewrite code in my htaccess file which converts all requests for index.php to /, and it works great, however I lose the capacity to make edits and the search feature doesn't work. Has anyone ever attempted this before?