Resolve issue with bundle format and caching

This adds a new internal concept of a `CachedModule` which is a subclass of
es6-module-transpiler's `Module` class. This is used during rebuilds to speed
up the "visiting" of unchanged modules.

Previously there was an issue when using the Bundle format, which would cause
the `id`'s of cached modules to grow and become out-of-wack. This fixes that.
Merge pull request #9 from ericf/cached-module

Resolve issue with bundle format and caching