This is pretty awesome and will be very helpful with large, enterprise applications, as well as applications that do many things that are not all related. I wonder if we could take this a bit further though...
Plugins, for example, extract themselves to the various locations (models, controllers, modules, views, static, etc). What if we allowed plugins to be better organized?. If I have a plugin called plugin_test, I would have a 'test' folder under the plugins folder, and in that folder I would have models, controllers, and views folders. This way, plugins can be a bit more 'pluggable' and self-contained instead of them merging with everything else. Would this be a good idea?