I don?t see how creating additional folders for navigation, hierarchical and structural purposes can at all conflict with the websites usability. Rather it would do the complete opposite; by logically organizing your website into subject areas you are ensuring that your users are ascertaining a better understanding of the websites layout.

Although I agree that for instance a good example of integration is Wordpress with vBulletin, Wordpress only requires a singular ./index.php page inside the forum root whilst the remaining configuration files can serve elsewhere in a ./blog/ folder for example. But unfortunately not all products are so forthcoming with their integration.

It makes much more sense for a website to be organised as so;
(BTW i am not very good with these virtual diagrams!)

Rather than the following;

1)__ What I mean by "usable" is that the URL is shorter ... therefore, easier to remember.
2)__ You are assuming that everyone wants a "blog", "gallery", and/or "portal".
3)__ All 3rd-party applications that you mentioned can work while vBulletin is in root.

thank you .. I didn't know that about WordPress
However, you just made my point -- if an application is well thought out you should never ever have to choose between "root" or "folder". The bad thing about WordPress is that it will take you time to learn, install, update, etc, etc. To me, all of this is "time" .. and time is money.

4)__ Like I said on my first post

Thank you :)