It's hardcoded in /library/XenForo/Dependenices/Public.php
A template edit alternative.
[CODE=rich]
<xen:if is="{$xenOptions.jQuerySource} == 'jquery'">
<xen:set var="$jQuerySource">//code.jquery.com/jquery-1.10.1.min.js</xen:set>
</xen:if>
<script src="{$jQuerySource}"></script>
<xen:if is="{$jQuerySource} != {$jQuerySourceLocal}">
<script>if (!window.jQuery) { document.write('<scr'+'ipt type="text/javascript" src="{$jQuerySourceLocal}"><\/scr'+'ipt>'); }</script>
</xen:if><xen:if is="{$xenOptions.uncompressedJs} == 1 OR {$xenOptions.uncompressedJs} == 3">
<script src="{$javaScriptSource}/jquery/jquery.xenforo.rollup.js?_v={$xenOptions.jsVersion}"></script></xen:if>
<script src="{xen:helper javaScriptUrl, '{$javaScriptSource}/xenforo/xenforo.js?_v={$xenOptions.jsVersion}'}"></script>
<!--XenForo_Require:JS-->[/CODE]
If the source is set to jQuery it uses the // prefix which should work on either http or https.
