g1smd - 1:36 am on Dec 18, 2012 (gmt 0)

removing index.php from the URL

URLs are defined in links on the page, so what you are literally asking is "I want to alter the links on my page from <a href="/index.php/pagename"> to <a href="/pagename">" yet you also say "none of my pages have ever linked to a URL with index.php in it".

So I am not sure "where" you want to remove it from, if it's not from the links on your pages.