[development] Move all core modules into their own directories.

[Robert Douglass]

Neil Drumm wrote:
> I would actually be okay with removing the whole engine system and 
> simply doing PHPTemplate only. Sure theme engines are a nice feature, 
> but how many are maintained and what % of themes are PHPTemplate?

I don't use anything but PHPTemplate, but I think that we want to keep 
the engine system. Why don't we just leave the theme_ function inclusion 
mechanism to the engine? PHPTemplate will require separate files, and 
other engines can do what they please.