Using Telnet or SSH to delete file If you have a command-line login (telnet or ssh), you can enter the following commands to make backup copies of the files you need to keep and to delete ONLY the wordpress files in your directory (plus .htaccess). If you’ve customized other files (like index.php) not included by the cp commands below, copy them as well:
mkdir backupcp wp-config.php .htaccess backupcp -R wp-content backuprm wp*.php .htaccess license.txt readme.html xmlrpc.phprm -rf wp-admin wp-includescp backup/wp-config.php .
After you have finished with the upgrade, you can restore any customizations to your templates or plugins from your backup directory. For example, use cp backup/index.php . to restore index.php.
Alternatively, using SSH, you could copy wp-config.php, .htaccess, and any content files you’ve added or altered into the newwordpress directory. Then, rename the old one (to archive it), and move the new one into its place.