TYPO3 Core

you can override it with TS as you can see in fluid/configuration/typoscript/setup.txt

-------------
page.headerData.998 = TEXT
page.headerData.998.value (
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js&quot;&gt;&lt;/script>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.4/jquery-ui.min.js&quot;&gt;&lt;/script>
<link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.3/themes/base/jquery-ui.css&quot; type="text/css" media="all" />
<link rel="stylesheet" href="http://static.jquery.com/ui/css/demo-docs-theme/ui.theme.css&quot; type="text/css" media="all" />
)
------------

Thanks Ringer Georg.

Found the solution of the extension html5_readykit for it - without testing it seems the protocol is prepended automatically there.

###### FLUID TEMPLATE HANDLING #####
[globalVar = LIT:1 = {$plugin.html5_readykit.useFluidTemplate}]
#Remove fluid scripts from header
    page.headerData.998 = TEXT
    page.headerData.998.value (
)

# Include jQuery from Google Libraries API
page.includeJS{
    # Add jQueryUi script
    jqueryui = //ajax.googleapis.com/ajax/libs/jqueryui/1.8.14/jquery-ui.min.js
    jqueryui.external = 1        
}

# Include CSS files
page.includeCSS{
    # Add jQueryUi css and jQuere Theme css
    jqueryui = //ajax.googleapis.com/ajax/libs/jqueryui/1.8.14/themes/base/jquery-ui.css
    jqueryui.external = 1

    jquerytheme = //static.jquery.com/ui/css/demo-docs-theme/ui.theme.css

    jquerytheme.external = 1        
}
[global]