What I do for my production apps is. For dev, i simply use all the individual files. For staging, I minify and concatenate and push it to an S3 bucket, and read it directly from there. For production, on CDN, because of caching, I add a version number to my js and css file name. This way I alway s guarantee that the user is using the correct version of my client code. I have grunt tasks to do all of these automatically, and it has worked really well for me.
Regarding hosting an Ember app, can you use something like s3 with cloudfront or will it not refresh fast enough to be usable?