Fix standardization scripts

## Simplify the process for everyone

Let's narrow this down to two commands whenever anyone wants to join this project.

* `script/setup` is for first time joiners, 
  * it basically is `script/bootstrap` but it would contain any initialization for the project outside of the Ruby (or other) environment.

* `script/server` 
  * runs `script/update` (which runs bootstrap) to contain all of the things that need to happen when you jump back into a project and need to make sure it's up to date. for teach.github.com, this is mostly trivial but habit forming.
  * Also launches the server with acceptance of additional flags.