Upgrade javascript libraries to current versions

Upgraded:
- jQuery to 1.11.0 (from 1.8.3)
- BackboneJS
- UnderscoreJS
- RequireJS
- Bootstrap
Fix models/views/collections to correctly init

I don't know how this worked before, but apparently it did.
Even some files had 'initialize' misspelled.

Fix initialization of variables, especially the use of
`this.options`

These errors weren't caught before, because magically things
worked with old versions of the libraries.  As the libaries
were upgraded, it exposed these issues.