Changing my original siteindex to use the new url rewritting of Geeklog 1.3.9 is very easy.
Change the original line 70 from
$display .= '<a href="' . $_CONF['site_url'] . '/article.php?story=' . $A['sid'] . '">'
to
$display .= '<a href="' . $_CONF['site_url'] . '/article.php/' . $A['sid'] . '">'
TomW