module directory parsing command option

This option allows the commandline ability to convert a directory of ES6 modules, into an output directory of transpiled modules. The module files remain distinct:

```
  traceur --dir app app-built
```

This then naturally allows the ability to transpile a directory full of ES6 modules into AMD ES5 modules:

```
  traceur --dir app app-built --modules=amd
```

Then does what we want!

Review URL: https://github.com/google/traceur-compiler/pull/686

Closes #686.