This file integrity checker uses Alternate Data Streams to store the hashes of your files. So, it only works on NTFS volumes. With that, you can rename, copy or move your files (to another NTFS volume) without losing the hashes, and without needing to do anything else.
The hashes are made with a 64-bit optimized version of the Whirlpool algorithm, which can currently process up to 147 MB/s with a Core I7 2600. Each folder is recursively processed. You can use drag-and-drop and mix files and folders. Because of its very low performances, 32-bit version is not recommended and is only provided for compatibility.
Whirlpool File Checker - 64bit software