Renamed 'app' to 'atc'
Added mathjax config and pulls from CDN
Move config files into separate dir

Also, simplified loading the aloha config
Added docco to dev dependencies
Removed repo sync call
Added build instructions
Removed custom URLs
Remove more custom URLs
Remove unnecessary layout regions
Added instructions for generating documentation
Updated documentation
Updated empty navTree bug
Changed how deferred loading works
Allow extending a Book
Allow subclassing the manifest in a book

(list of content items the book should listen for changes in)
Refactored extension point for supporting multiple media types
Added models that parse/serialize to valid epubs
Updated XHTML edit action
Loading data is now silent
Loading data is now silent