drupal_add_js in html template file
You can try to insert the JS files by the preprocess function in your theme's template.php file:

Here goes an example:

function MYTHEME_preprocess_page(&amp;$variables) {
  drupal_add_js(drupal_get_path('theme', 'MYTHEME') .'/mytheme.js', 'file');
}


You can use an if() to validate the current path in the $variables in order to prevent the script to be loaded on every page.

To debug the $variables values you can install the devel module an use the dpm() function.

For example:

function MYTHEME_preprocess_page(&amp;$variables) {
  dpm($variables);
}