Empty space instead of admin bar

you are correct, that is for the admin bar. add this code to functions.php to disable the admin bar if you wish <?php /* Disable the Admin Bar. */ remove_action( ‘init’, ‘wp_admin_bar_init’ ); ?> if you want to use it then check your source for <div id=”wpadminbar”> <div class=”quicklinks”> If so, then the output is … Read more

3.1.3 auto-upgrade

sounds like you need to think about a new host… do I dare ask where you’re hosted now? But yes that’s a permission issue.

Getting rid of files not used by latest upgrade

For several versions already core updates are partial (differential). Only changed files are downloaded and overwritten so it is not safe to assume that those that weren’t are not used. However, you can compare downloads of two full releases to see which file aren’t used any more.