I chose to keep the sprockets functionality by changing
//= require_tree
to
//= require_directory .
This keeps sprockets auto-loading any files in the same directory, but not in any folders further.
This allowed me to move Modernizr.js to the assets/javascripts/top folder and manually load it at the top with:
<%= javascript_include_tag "top/modernizr" %>
and move
<%= javascript_include_tag "application" %>
To the bottom of my application.html.erb file (above the closing body tag)
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