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Any non-trivial application will contain more than one code file. What is the Ember.js solution for this? Makefiles? And what about HTML? I'd like to organize those by sections of the app. How is that achieved?

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I'd recommend rake-pipeline: http://github.com/livingsocial/rake-pipeline

Most of the Ember apps I'm aware of are using it.

Also, you might want to check out rake-pipeline-web-filters for additional functionality: https://github.com/wycats/rake-pipeline-web-filters

That looks pretty awesome, thanks. However I feel like this is something the framework should handle for the basic use cases. Learning rake-pipeline is probably worth the effort but should never be required. Developers should spend their time thinking about their app, not deployment details.

Check out slinky[0], which in addition to solving the minification/concatenation issue for JS/CSS also does compilation of CS/HAML/SASS and provides a proxying development server. It's designed sort of in the mold of the sproutcore build tools, but unconnected to any particular client side framework.

[0] https://github.com/mwylde/slinky

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