Here's my quick hack:
--- theme.php ---
// Javascript + jQuery
function js_scripts( $jsbla ) {
$jsbla .= "<!--[if lt IE 8]>\n";
$jsbla .= "<script type=\"text/javascript\" src=\"".THEMEJS."/ie.js\"></script>\n";
$jsbla .= "<![endif]-->\n";
$jsbla .= "<script type=\"text/javascript\" src=\"".THEMEJS."/jquery.js\"></script>\n";
$jsbla .= "<script type=\"text/javascript\" src=\"".THEMEJS."/script.js\"></script>\n";
return $jsbla;
}
add_filter( 'framework_head_js', 'js_scripts' );
--- general-template.php ---
$stylesheets .= apply_filters( 'framework_head_css', (string) '' ); // Available filter: framework_head_css
$stylesheets .= apply_filters( 'framework_head_js', (string) '' ); // Available filter: framework_head_js