Friendly URL and Alias HELL

I want to use friendly URL and alias also to hide the directory structure of my website, since is one of the main reason to use friendly URL

everything works (with RewriteRule and so on... thanks to TobyL for the advices for the non-modx subdomain)

but modx keep on writing URL using the real path, i.e.

www.mysite.com/index.php

is, in fact,

www.mysite.com/modx/index.php

but the links on this page are all

www.mysite.com/modx/4.html and so on

I would like to have the links

www.mysite.com/4.html (and the rewriterule will correctly rewrite it to www.mysite.com/modx/4.html)