Hey that's good to hear.
I'm very glad to hear that it works, there's another guy who's trying to get it working and it's an endless story, I'm about to give up. So tell me, which nodejs are yo running, is it nodejs v.4 ?
The architecture is different from the simple starters, but it's not that strange. The well-known AngularJS expert John Papa is one of the people who recommend this structure, see this description in his famous Style Guide:
https://github.com/johnpapa/angular-styleguide#style-y152
It's called "directory per feature" (or module) and is better suited to larger apps (the structure in the default starter apps doesn't scale well to larger apps, lumping everything in 3 Javascript files isn't really a good idea).
I've also described the structure in the README file:
https://github.com/leob/ionic-quickstarter#project-structure
Just read that section (and maybe also the John Papa link that I gave you) and I am sure it will become all clear.