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It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

Find page.xml of your theme and find the following

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">

And insert the following just before :

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
   <action method="addJs"><script>your_script.js</script></action>
</block>

For Magento 1.9 use this:

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
       <action method="addItem"><type>skin_js</type><name>js/yourskinfile.js</name><params/></action>
    </block>

Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following

<?php echo $this->getCssJsHtml() ?>

Add below in your template just before closing </body> tag.

<?php echo $this->getChildHtml('jsfooter') ?>

It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

Find the following line in page.xml of your theme

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">

And insert the following just before :

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
   <action method="addJs"><script>your_script.js</script></action>
</block>

For Magento 1.9 use this:

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
       <action method="addItem"><type>skin_js</type><name>js/yourskinfile.js</name><params/></action>
    </block>

Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following

<?php echo $this->getCssJsHtml() ?>

Add below in your template just before closing </body> tag.

<?php echo $this->getChildHtml('jsfooter') ?>

It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

Find page.xml of your theme and find the following

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">

And insert the following just before :

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
   <action method="addJs"><script>your_script.js</script></action>
</block>

Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following

<?php echo $this->getCssJsHtml() ?>

Add below in your template just before closing </body> tag.

<?php echo $this->getChildHtml('jsfooter') ?>

It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

Find page.xml of your theme and find the following

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">

And insert the following just before :

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
   <action method="addJs"><script>your_script.js</script></action>
</block>

For Magento 1.9 use this:

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
       <action method="addItem"><type>skin_js</type><name>js/yourskinfile.js</name><params/></action>
    </block>

Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following

<?php echo $this->getCssJsHtml() ?>

Add below in your template just before closing </body> tag.

<?php echo $this->getChildHtml('jsfooter') ?>

It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

open the page.xml from your theme layout files and do following

<!-- find the following line -->
<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">  
</block>

Modify as follow :

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">  
   <!-- here we are adding a javascript -->
   <action method="addJs"><script>your_script_here.js</script></action>
 </block>

To remove javascript from the head

<!-- open the page by source view and locate the script lines the put script_name -->
<action method="removeItem"><type>js</type><name>calendar/calendar.js</name</action>

Try and let me know the result

It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.

To moving the script :

Find page.xml of your theme and find the following

<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">

And insert the following just before :

<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
   <action method="addJs"><script>your_script.js</script></action>
</block>

Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following

<?php echo $this->getCssJsHtml() ?>

Add below in your template just before closing </body> tag.

<?php echo $this->getChildHtml('jsfooter') ?>