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
Merge master