Removed unneeded javascript files
Misc Tweaks
Added comment hooks to comments.php
Added comments hooks to functions file
Added comments hooks tests
Added notes about default content for Comments hooks
Update html5shiv to 3.7.2
Updated JS loading for HTML5 Shiv, Respond.js and Modernizr
Simplify how Sidebars are registered and created
Remove files/calls to custom post types and taxonomies

These should be in plugins, not the main theme
Significant re-factor of theme functions file
Remove shortcodes because we're not using yet
Simplify comments
Break out Comments functions into separate file
Clarifying comment on Hooks tests
Move image attachment handling function to images setup
Whitespace alignment tweak
Add hooks & tests to individual comment entries
Misc Whitespace tweaks