Folder nesting doesn't need to be too deep.. About a depth of 3 is probably more than enough; provided there's some top level grouping*. Any more; it is just over-classification, that could probably be better solved by tighter / stricter classification.

I gotta say, there's a big difference between centralizing the application and centralizing the navigation experience / interface about an all serving singularity.. The application can be centralized and act upon a distributed collection of files as they are requested; by means of handlers; even mod_redirect. That's quite different from using one script as the means of serving all requests; it's certainly my prefered technique =P. Hey; I'd rather not go too far divulging my own behind-the-scenes work; but I use that as a way of getting the best of both worlds - I can keep my application high up in /home/me; but still use it to process XML-based scripts in any folder a user requests... as long as the file ends '.xrm'.

Hey... with Java; it's worth the trade-off sometimes. Other times; perhaps not. The whole Java structure-of-an-application, although rigid, affords flexibility; and forces a developer to conform to good organisation practises ( hey; that's an opinion =P ). C++ is a more interesting language for sure; but Java is a powerful language in terms of capability; and the fact it doesn't need to be recompiled for every target OS is a huge advantage in my eyes.

Hm.. C++ Templates whup Java Generics 10 times over though..

* by "top level grouping"; I mean grouping into 'public_html', 'cgi-bin' etc if we're on Apache.. gawd knows what MS server OS's do... My Documents?..