Document and Refactor

This is the first batch of documentation and refactorings of Omnibus.  The main code change here lies around how Omnibus is configured.  Before, it would require some configuration in an `omnibus.rb` file, as well as some additional Ruby in the project's Rakefile to pull in omnibus-software and allow project software to override omnibus-software definitions.  That's all pulled into Omnibus proper now; if omnibus-software is in the gemfile, it is assumed that you want those definitions pulled in.  Furthermore, it is assumed that if you have identically-named software definitions in your project, they should supersede the stock ones from omnibus-software.

As a happy consequence, all you'll generally need to do in your Rakefile to configure Omnibus now is 

```ruby
Omnibus.configure
```
There are several "todo" comments for future refactorings... comments welcome.