This post assumes you have your moodle site files in /var/www directory and the moodle folder renamed to moodlesite on your Ubuntu linux server
cd /var/www/
# Rename current moodle directory to moodlesite_bak
mv moodlesite moodlesite_bak
# Extract fresh Moodle to original folder
tar -xvzf /tmp/moodle-latest-403.tgz -C /var/www/
mv /var/www/moodle /var/www/moodlesite
# Copy config.php from old to new
cp /var/www/moodlesite_bak/config.php /var/www/moodlesite/
# Copy custom plugins or themes if any
cp -r /var/www/moodlesite_bak/local/* /var/www/moodlesite/local/
cp -r /var/www/moodlesite_bak/theme/* /var/www/moodlesite/theme/
cp -r /var/www/moodlesite_bak/mod/* /var/www/moodlesite/mod/ # Only custom ones!
# Set proper permissions
chown -R www-data:www-data /var/www/moodlesite
#Then upgrade site and purge caches
sudo -u www-data php /var/www/moodlesite/admin/cli/upgrade.php
sudo -u www-data php /var/www/moodlesite/admin/cli/purge_caches.php