I assumed the project root folder is in /public_html/magento/
Copy the js file into:
/public_html/magento/js/yourSubFolder
Tell about this to :
/public_html/magento/app/design/frontend/base/default/layout/page.xml
add this line to
<block type=”page/html_head” name=”head” as=”head”>
section
<action method=”addJs”><script>nhdGallery/scripts.js</script></action>