Comment on Remove WordPress Meta Generator Tag by SEO Dave.

WordPress Readme HTML Looks like the code is used for the WordPress single page next and previous links and the next and previous links for archives (categories navigation etc…).

Top is for single, bottom archives, either delete the reference to this file on single.php

<?php include (TEMPLATEPATH . "/bot-nav.php"); ?>

Or change the code you posted to:

<div class="navigation clearfix">
<?php if ( is_single() ) { ?>
<?php } else { ?>
<?php if ( function_exists('wp_pagenavi') ) { ?>
<?php wp_pagenavi(); ?>
<?php } else { ?>
<?php posts_nav_link(); ?>
<?php } ?>
<?php } ?>

That deletes the next/prev links from single.php posts only leaving the archive next/prev links in place.