Just to save you from having to scroll (that’s a long and complex article), I’ll post Step 7 here for you, that’s how important I think it is.
Step 7: Delete the old WordPress files
Why Delete? Generally, it is a good idea to delete whatever is possible because the uploading (or upgrading through cPanel) process may not correctly overwrite an existing file and that may cause problems later.
DO NOT DELETE these folders and files:
* wp-config.php file;
* wp-content folder;
* wp-images folder–only older installations from 1.5.x days will have this folder;
* wp-includes/languages/ folder–if you are using a language file, and it is here rather than in wp-content/languages/, do not delete this folder (you might want to move your language files to wp-content/languages/ for easier upgrading in the future);.
* .htaccess file–if you have added custom rules to your .htaccess, do not delete it;
* Custom Content and/or Plugins–if you have any images or other custom content or Plugins inside the wp-content folder, do NOT delete them.
Delete these Files and Folders:
* wp-* (except for those above), readme.html, wp.php, xmlrpc.php, and license.txt; files; Typically files in your root or wordpress folder. Again, don’t delete the wp-config.php file.
* wp-admin folder;
* wp-includes folder; If you have a language file here, remember not to delete the wp-includes/languages/ folder
* wp-content/cache folder; You only see this folder if you are upgrading FROM WordPress 2.0.
* wp-content/plugins/widgets folder; You only see this folder if you previously installed the Sidebar Widgets plugin. The Sidebar Widgets code conflicts with the built-in widget ability.
