How to add all existing js files which we see after page source of home page, before end of the body tag in magento ?

Answer 1

Put the JS file somewhere into the "js" folder, and in the XML layout you can include it with:

<reference name="head">
    <action method="addJs"><script>folder/file.js</script></action>
</reference>

Edit: You can also do it in your block:

protected function _prepareLayout()
{
    $this->getLayout()->getBlock('head')->addJs('path/from/js/folder/to/your/file.js');

    return parent::_prepareLayout();
}