A Magento 1 script that will only reindex and refresh caches that have been invalidated.

magentoSmartIndexCacheRefresh.sh

#!/bin/bash

# Smart Magento reindexing and cache clearing.  Only indexes and caches that are
# invalidate are cleared.  Place this file in your shell/ directory and make it
# executable: chmod +x magentoSmartIndexCacheRefresh.sh
# 
# Before use it is recommended to consider your failures as a developer due to
# lack of ability to correctly update individual indexes and caches as records
# modified processed.
# 
# Usage:
#     $ cd /var/www/html/magento
#     $ ./shell/magentoSmartIndexCacheRefresh.sh
# 
# Or cron:
#     */5 * * * * cd /var/www/html/magento && ./shell/magentoSmartIndexCacheRefresh.sh >> /var/www/html/magento/var/log/smart-index-cache.log
#
# Or lazy daemon:
#     $ screen
#     $ watch -n 5 "cd /var/www/html/magento && ./shell/magentoSmartIndexCacheRefresh.sh"
#     CTRL+d
#

BIN_PHP=`which php`
BIN_GREP=`which grep`
BIN_PS=`which ps`

DIR_SHELL=`echo $0 | sed 's/magentoSmartIndexCacheRefresh\.sh//g'`

magentoPhp() {
    $BIN_PHP -r "require '$DIR_SHELL../app/Mage.php'; Mage::app(); $1"
}

reindex() {
    magentoPhp "foreach(Mage::getSingleton('index/indexer')->getProcessesCollection() as \$p) { if (\$p->getStatus() == Mage_Index_Model_Process::STATUS_RUNNING) { continue; } \$p->indexEvents(); if (\$p->getStatus() != Mage_Index_Model_Process::STATUS_REQUIRE_REINDEX) { continue; } \$p->reindexEverything(); Mage::dispatchEvent(\$p->getIndexerCode() . '_shell_reindex_after'); echo 'Reindexed ', \$p->getIndexerCode(), PHP_EOL; }"
    if [ $? -eq 0 ]; then
        echo "Required indexes reindexed"
    else
        echo "There was a problem while reindexing"
    fi
}

clearCache() {
    magentoPhp "foreach(Mage::app()->getCacheInstance()->getInvalidatedTypes() as \$k => \$c) { Mage::app()->getCacheInstance()->cleanType(\$k); echo 'Cleared ', \$k, PHP_EOL; }"
    if [ $? -eq 0 ]; then
        echo "Required caches cleared"
    else
        echo "There was a problem while clearing caches"
    fi
}

if ! $BIN_PS aux | $BIN_GREP "${DIR_SHELL}magentoSmartIndexCacheRefresh.sh" | $BIN_GREP -v grep | $BIN_GREP -v "$$" | $BIN_GREP -v watch | $BIN_GREP -v "sh -c" 1>/dev/null 2>/dev/null ; then
    reindex
    clearCache
else
    echo "Script is already running.  Not executing."
fi