I just answered a similar question on Drupal Answers: https://drupal.stackexchange.com/questions/46202/move-aggregated-js-file-to-the-footer/89590#89590
I will copy the answer below for quick reference.
, , Drupal Answers , , - , , . .
Drupal 7: https://gist.github.com/pascalduez/1418121
$ script $head_scripts, , JS . , Modernizr .
, .
.
html.tpl.php
<!DOCTYPE html>
<html<?php print $html_attributes; ?>>
<head>
<?php print $head; ?>
<title><?php print $head_title; ?></title>
<?php print $styles; ?>
<?php print $head_scripts; ?>
</head>
<body<?php print $body_attributes;?>>
<?php print $page_top; ?>
<?php print $page; ?>
<?php print $scripts; ?>
<?php print $page_bottom; ?>
</body>
</html>
template.php
function THEMENAME_preprocess_html(&$vars) {
$path = drupal_get_path('theme', 'THEMENAME');
drupal_add_js($path . '/js/modernizr.min.js', array('scope' => 'head_scripts', 'weight' => -1, 'preprocess' => FALSE));
}
function THEMENAME_process_html(&$vars) {
$vars['head_scripts'] = drupal_get_js('head_scripts');
}