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.
@rwjblue right now, during rebuilds, you can end up in a situation where the bundle format is broken. This address that in a cleaner way then what we had before while not incurring unnecessary file IO. As @mmun mentioned, I want to get to where we can cache the AST, but do so in a way that's both safe and not a hack.