Look at the file app/design/frontend/<yourlayout>/<yourtheme>/layout/page.xml (or copy app/design/frontend/base/default/layout/page.xml to your theme).
Inside this file, find the following lines:
<block type="page/html_head" name="head" as="head"> <action method="addJs"><script>prototype/prototype.js</script></action> </block>
And change addJs to:
<block type="page/html_head" name="head" as="head"> <action method="addJs"><script>prototype/prototype.js</script><params>async</params></action> </block>
Since you use the javascript magento merge function, you need to apply this change to each addJs definition, since Magento will group files using params .
GiDo
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