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JS Builder will parse all your JS files, resolve dependencies between module, merge and optimise the files into one, always ensuring that the correct load order is maintained relative to any dependencies. You can also build in 'dev' mode where it will output all the files separately.
This is a very new project and the current code base is somewhat mucky, but it is doing the job as a proof of concept. Will be improving it over the coming days and would be good to see what people think!