The Mage Project Integrity Checker checks a magento install for modified core files for Magento Community editions without having to download a base copy to compare it to. The comparison files are downloaded directly from this repo as needed by the script. The comparison files for Magento 1 versions are also based off of installs that are fully patched.
The mageintegriycheck.php file is the only requirement to use.
Usage: php mageintegriycheck.php
Any modified core file will be returned.
Updated 9/6/17: Added support for latest magento versions