Too many opinions and suggestions are worse than none.
IMHO developers either know and understand Apache rewrites like the back of their hand, or not at all. It is a bit of an obscure art, as the need for it does not tend to pop up every day.
Yet I was determined that going forward "index.php" in urls would not be tolerated. A url that includes "index.php" presents a dated site appearance to the few who notice. More importantly, eliminating it frees up 8 characters in a space better used for SEO.
The below is tested and proven to work with eZ Publish 4.4 on Media Temple DV servers up to DV 4.0
1. At install time, remove the "index.php" from the default access urls for users and admin
2. In /settings/override/site.ini.append [SiteAccessSettings] add line - ForceVirtualHost=true
3. .htaccess file looks like this
RewriteEngine On
RewriteRule content/treemenu/? index_treemenu.phpRewriteRule ^index_treemenu\.php - [L]
RewriteRule !(\.(gif|jpe?g?|png|css|js|swf|html?)|var(.+)storage.pdf(.+)\.pdf)$ index.php
DirectoryIndex index.php
Caveat
The admin pages are no longer accessible from the link prepared by the installer. The admin pages are accessible using a "short" path of <domain>/<admin-name-from-installer>. In my case http://nbmpa.org/nbmpa_admin, with nbmpa_admin being the name I used for the administrator at install time.
No index.php in the url, yeah!