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Take a look in build.default.json
You can see how *.es6 files are handled by default in this file: a requirement is declared to node, babel and webpack (currently without any particular version constraint), and the webpack command is executed, passing arguments to compile the main.es6 entry-point script to an output file at www/script.js.
The purpose of the arguments passed to webpack are to produce a single, fully contained compiled JavaScript that requires no extra frameworks to "require" scripts, etc.
I have not personally used TypeScript for anything non-trivial, so I'm hoping someone else can offer some help on this issue. I would like to see the entry point main.ts compiled to www/script.js.