JavaScript clean up

- Modernizr is now enqueued and included after stylesheets

- jQuery is no longer hardcoded since WP now supports protocol-relative
URLs

- jQuery fallback output is handled by a new function in lib/scripts.php
(the method is still the same one from HTML5 Boilerplate)
Update comment about jQuery
Allow get_search_form() to be called more than once per request
Change JS ordering

- Load jQuery before Modernizr so that the fallback method will
always be applied immediately after jQuery. If a script is
enqueued in the footer after jQuery, then the fallback shows up
in the footer. Modernizr will always be in the head so this
issue won't occur.

- Move plugins.js and main.js to footer

jQuery is still kept in the head to avoid conflicts with plugins
Simplify entry meta
Fix #639 - Add do_action('get_header')
Don't show comments on passworded posts
Update included H5BP .htaccess

- Add latest updates from H5BP

- Remove various parts that were previously commented out
Update 404 template based on H5BP
Add EditorConfig
Fix #677 - Output author title with get_the_author
Close #670 - Update to jQuery 1.9.1
Update CHANGELOG
Update to Bootstrap 2.3.0
Roots 6.3.0
Static top navbar instead of fixed

This change allows us to simplify the code in both
app.css and cleanup.php