Refactor GEPPETTO modules to AMD format

* GEPPETTO modules refactored to AMD, encapsulated to provide a private namespace for local vars and functions. Modules that reference the application object define a function to which can be passed the application object at the time of initialization:

     require('module')(GEPPETTO);

     Note that within a module, you cannot safely execute code involving other modules at the time of initialization.

* Variables and modules removed from global namespace wherever possible, moved to GEPPETTO.[module].[variable]. Variables that must be global are aliased to global namespace in main.js. Plots are also still being put in the global namespace by name (I.e. "Plot1", "Plot2", etc.). 

* Require.js configs changed: Modules are imported at time of use where possible, and AMD modules have been removed from the shim. 

* SandboxConsole fixed to work with Backbone v1.1.7 (Please test, I'm not sure what the exact desired functionality is.)

* General cleanup elsewhere. 

PLEASE TEST