First build needs node_modules/src/node files.

Fixes #682

TBR=@arv

Review URL: https://github.com/google/traceur-compiler/pull/685

Closes #685, closes #682.
Define ModuleStore and System.

Rename modules.js -> ModuleStore.js.
Former System now ModuleStore.
System now an instance of Loader.
Forward get/set/normalize through Loader/LoaderHooks/ModuleStore.

Review URL: https://github.com/google/traceur-compiler/pull/679

Closes #679.
--dir option for compiling a directory of modules into AMD or CommonJS