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.
> I do worry that we shouldn't be optimizing the bundled output for rebuilds/development, but rather the the 1-1 formatters.

@mmun I thought the same, but then realized that with source maps, using the an n-1 formatter, like the bundle format, during development is fine and actually easier than using a 1-1 formatter.