Speed up bootstrap by using checksums

We've been using this modified bootstrap here at GitHub for months. I've
neglected to extract it to the public repo, until now.

This uses a quick checksum of `Gemfile`, `Gemfile.lock`, binstubs, the
ruby version and bundler version to determine if bundling is
necessary. This is much, much faster than running bundler every time.

I've also included some of our other misc. changes, mainly to logging
output and some minor structural pieces.
Merge pull request #665 from boxen/speedup-bootstrap

Speed up bootstrap by using checksums