Which version of Geeklog are you talking about? Geeklog v2.2.1 and sr1 shipped with the correct version of jQuery that was defined in the resource class.
The r.php is used by /system/classes/Resource.php
For jQuery you have the option to use the CDN option in the config set to true (Use CDN-hosted copy of jQuery and uikit).
Else it should default to using jquery found in public_html/vender/jquery
Hmmm, I did just notice that we do still have an old copy of jquery and juqery ui located in public_html/javascript/
I have updated this issue: https://github.com/Geeklog-Core/geeklog/issues/1059
to make sure this old version gets removed.
One of the Geeklog Core Developers.