Basically, it's a minimal Rails-API app (based loosely on this gist) embedded in an api folder in the root. Then the rest of it is a stock ember-cli setup. I don't know yet exactly how to make Rails look elsewhere for initializers, environments & locales, going to look into it.
api/ *.rb
controllers/
models/
initializers/
environments/
locales/
config.rb
routes.rb
app/ *.js
controllers/
models/
styles/ *.{scss,less,styl,etc}
router.js
app.js
config/
environments/
adapters/ (currently under app in ember-cli, talking to @stefanpenner about moving them)
serializers/
transforms/
...