Looks like the directory structure (in lib/...) is related to the use of component.io? [for app components].
I typically build node apps with application "modules" in an apps/{name} structure and then require them all in server.coffee.
Component.io is new to me, it claims to provide an entire "bundle" of client & server side pieces, this is nice. I'll have to look into that today ...
Definitely, an explanation of these "best practices" would be nice.