Bundle format fixes

This fixes two major issues which make the current bundle format break:

1. Fixed the `mkdirp.sync()` call from 2ca75d52 to make sure to get the path's dir.
2. Properly handle rebuilds that output to the bundle format by using a safer caching strategy.

The major change here is updating to `es6-module-transpiler@0.6.2` which now has a hook for controlling file IO on the internal `Module` class instances. This allows for a **much safer** _and_ simpler caching strategy for keep re-builds from needing to perform file IO on unchanged modules.
@ericf explained to me the cost: every file that has changed AND all the files it depends on (I assume that means all the module that this module imports) must be reparsed.

This change need not be permanent. We can recover the AST caching when recast implements a cloning mechanism.

I worry that we shouldn't be optimizing the bundled output for rebuilds/development, but rather the the 1-1 formatters.