Sooo, I’ve just recently jumped into Ember — and directly into Ember CLI. The thing is awesome, but what has really bugged me from the start is the one-class-per-file convention enforced by the module resolver. I often prefer to deal with a bunch of related classes as a combined unit, and in all likelihood there are many others who share this sentiment.
As a result, I wrote a custom resolver that allows me to group multiple classes into consolidated modules that live on some parent level in the source tree.
If you’re using Ember CLI and grappling with an escalating number of files and endless subdirectories, you might find my Magic Resolver useful: https://github.com/bintoro/ember-magic-resolver.