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.
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.
Fix issues with labels in generators

- All named break and continue statements need to be transformed into a state machine
- The way that labels where propagated down was not correct

Fixes #605

Review URL: https://github.com/google/traceur-compiler/pull/680

Closes #680, closes #605.
AMD __transpiledModule flag for System loader transpilation support

To explain the feature, the reason for this is I want to be able to dynamically load AMD from ES6 Module Loader, but also support loading AMD that is compiled from ES6 and should be treated like an ES6 module.

In this way, one can write ES6 modules, then transpile them back into AMD for production, and have the `System` loader behave identically, just without the Traceur step.

But, in order to distinguish handling between an AMD module and an ES6 in disguise as an AMD module, we need to have some kind of flag to know that we should treat it as the module object directly:

```javascript
  new Module(amdExport)
```

instead of using the `default` property of a module, which is done for AMD exports normally for compatibility:

```javascript
  new Module({ default: amdExport })
```

Suggestions welcome if there are better ways of going about this.

Review URL: https://github.com/google/traceur-compiler/pull/683

Closes #683.
Correct make dependencies for src/codegeneration/modules and to fire npm install on make clean.

Sync up bin/traceur.js

Review URL: https://github.com/google/traceur-compiler/pull/687

Closes #687.
Merge remote-tracking branch 'upstream/master' into annotations

* upstream/master:
  Correct make dependencies for src/codegeneration/modules and to fire npm install on make clean.
  AMD __transpiledModule flag for System loader transpilation support
  Fix issues with labels in generators
  module directory parsing command option
  Define ModuleStore and System.
  First build needs node_modules/src/node files.

Conflicts:
	bin/traceur.js
Code review cleanup.  Added test for parse error on invalid annotated expression.