Use: update.sh /absolute/path/of/your/OpenCart/installation. Read this post for details: http://easywebthings.blogspot.com/2015/10/opencart-upgrade-script.html

OpenCart update script

#!/bin/bash

RED='\033[0;31m'
YELLOW='\033[0;33m'
GREEN='\033[0;32m'
NC='\033[0m' # No Color

dest=$1

keep_local=(
    ".git"
    ".gitignore"
    ".idea"
    ".htaccess"
    "config.php"
    "admin/config.php"
    "catalog/view/theme/my_custom_theme"
    "image/cache"
    "image/templates/my_custom_logo.png"
    "system/storage"
    "image/catalog"
)

ignore_new=(
	".htaccess.txt"
	"config-dist.php"
	"admin/config-dist.php"
)

if [ -z "${dest}" ]; then
	echo -e "${RED}Please specify a destination directory.${NC}"
	exit 1
fi

last=${dest:${#dest}-1:1}
if [ "${last}" != "/" ]; then
	dest="${dest}/"
fi

if [ ! -d "${dest}" ]; then
	echo -e "${RED}Destination directory doesn't exists. Please specify a current OC installation.${NC}"
	exit 1
fi

if [ ! -f "${dest}/index.php" ]; then
	echo -e "${RED}${dest}/index.php has not been found.${NC}"
	echo -e "${RED}Please check if destination directory is a valid OC installation.${NC}"
	exit 2
fi

cur_ver=`grep -E "define\('VERSION', '[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+(_rc)?'\);" "${dest}/index.php" | sed -E 's/.*([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+(_rc)?).*/\1/g'`
echo -e "Current version: ${cur_ver}"

if [ -f source/upload/index.php ]; then
	read -e -p "Found a local distribution. Update? (y/N)" YN

	if [ "${YN}" != "y" ] && [ "${YN}" != "Y" ]; then
		rm -rf ./source
		echo -e "Checking new release..."
		git clone https://github.com/opencart/opencart.git source > /dev/null
	fi
fi

if [ ! -f source/upload/index.php ]; then
    echo -e "${RED}Cannot download a new OC release. Update failed.${NC}"
	exit 1
fi

cd source/upload

new_ver=`grep -E "define\('VERSION', '[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+(_rc)?'\);" "index.php" | sed -E 's/.*([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+(_rc)?).*/\1/g'`

if [ "${cur_ver}" == "${new_ver}" ]; then
	echo -e "${YELLOW}No new releases found.${NC}"
	read -e -p "Force upgrade? (y/N)" YN

	if [ "${YN}" != "y" ] && [ "${YN}" != "Y" ]; then
    	echo -e "Cancelled by user."
    	exit 4
	fi
fi

echo -e "${GREEN}New release version: ${new_ver}${NC}"

read -e -p "Procced to upgrade? (y/N)" YN

if [ "${YN}" != "y" ] && [ "${YN}" != "Y" ]; then
	echo -e "Cancelled by user."
	exit 4
fi

echo -e "Starting upgrade..."

delete_filter="diff -rq ./ ${dest} | grep \"Only in ${dest}\" | sed \"s/Only in //g\" | sed 's/: /\//g' | sed 's/\/\//\//g' | grep -Ev \""
for keep in ${keep_local[@]}
do
	delete_filter="${delete_filter}^${dest}$keep|"
done
delete_filter="${delete_filter}^${dest}stub\""

count=`eval ${delete_filter} | wc -l`

if [ "${count}" -gt "0" ]; then

	echo -e "${RED}Files to be removed:${NC}"

	eval ${delete_filter}
	YN=''
	read -e -p "Proceed to remove? (y/N)" YN

	if [ "${YN}" != "y" ] && [ "${YN}" != "Y" ]; then
    	echo -e "Cancelled by user."
    	exit 4
	fi

	delete_filter="${delete_filter} | xargs rm -rf"
	eval ${delete_filter}

	echo -e "${count} files were removed."
fi

echo -e "Copying new files..."
while true; do
	new_filter="diff -rq ./ ${dest} | grep \"Only in ./\" | sed \"s/Only in //g\" | sed 's/: /\//g' | sed 's/\/\//\//g' | grep -Ev \""
	for ignore in ${ignore_new[@]}; do
    	new_filter="${new_filter}^./$ignore|"
	done

	new_filter="${new_filter}^./stub\""
	count=`eval ${new_filter} | wc -l`

	if [ "${count}" -gt "0" ]; then

		items=`eval ${new_filter}`

		for item in ${items}; do
			if [ -d "${item}" ]; then
				mkdir -p "${dest}${item}"
			else
				cp "${item}" "${dest}${item}"
			fi
		done

    	echo -e "${count} new files were copied."
	else
		break
	fi
done

echo -e "Upgrading old files..."
upgrade_cmd="diff -rq ./ $dest | grep \" differ\" | sed \"s/ differ$//g\" | sed 's/: /\//g' | sed \"s/^Files //g\" | sed -E 's/^(.*) and (.*)$/cp \"\1\" \"\2\"; /g'"
count=`eval $upgrade_cmd | wc -l`
items=`eval ${upgrade_cmd}`
eval ${items}

echo -e "${count} files were upgraded."

echo -e "${GREEN}Upgrade finished!${NC}"