Simplified cache cleaning script for production updates.

cleanCache.php

<?php
/**
 * Set global/skip_process_modules_updates to '1' in app/etc/local.xml and
 * then use this script to apply updates and refresh the config cache without
 * causing a stampede on the config cache.
 *
 * @author Colin Mollenhour
 */
umask(0);
ini_set('memory_limit','512M');
set_time_limit(0);
if(file_exists('app/Mage.php')) require 'app/Mage.php';
else require '../../app/Mage.php';

// Init without cache so we get a fresh version
Mage::app('admin','store', array('global_ban_use_cache' => TRUE));

echo "Applying updates...\n";
Mage_Core_Model_Resource_Setup::applyAllUpdates();
Mage_Core_Model_Resource_Setup::applyAllDataUpdates();
echo "Done.\n";

// Now enable caching and save
Mage::getConfig()->getOptions()->setData('global_ban_use_cache', FALSE);
Mage::app()->baseInit(array()); // Re-init cache
Mage::getConfig()->loadModules()->loadDb()->saveCache();
echo "Saved config cache.\n";

It might also be necessary to recompile before applying updates. Something like this:

@include 'includes/config.php';
if (defined('COMPILER_INCLUDE_PATH')) {
    Mage::getModel('compiler/process')->run();
}

I've added an exit if the script isn't run on CLI and made an include that works when you place the script in the 'shell' folder:

<?php
/**
 * Set global/skip_process_modules_updates to '1' in app/etc/local.xml and
 * then use this script to apply updates and refresh the config cache without
 * causing a stampede on the config cache.
 *
 * @author Colin Mollenhour
 */
if(strtolower(php_sapi_name()) != 'cli'){
  exit;
}

umask(0);
ini_set('memory_limit','512M');
set_time_limit(0);

set_include_path(
    get_include_path() . PATH_SEPARATOR .
    dirname(dirname(__FILE__))
);

require_once('app/Mage.php');

// Init without cache so we get a fresh version
Mage::app('admin','store', array('global_ban_use_cache' => TRUE));

echo "Applying updates...\n";
Mage_Core_Model_Resource_Setup::applyAllUpdates();
Mage_Core_Model_Resource_Setup::applyAllDataUpdates();
echo "Done.\n";

// Now enable caching and save
Mage::getConfig()->getOptions()->setData('global_ban_use_cache', FALSE);
Mage::app()->baseInit(array()); // Re-init cache
Mage::getConfig()->loadModules()->loadDb()->saveCache();
echo "Saved config cache.\n";

NB The memory limit of 512 might be too low, you could always disable it (at your own risk) by setting it to -1.

It is important to note that you will still need to refresh the cache in the traditional way after running this script as any layout, ddl, block and possible other types of cache will not be up to date to the recently deployed code.