Version 1.0 was a brute-force version that ran checksums on every file in the specified directories.
Version 2.0 uses file size comparisons to greatly reduce the need for checksums. Tests on a variety of directories and file systems show it to be about 9x-11x faster than v. 1.0. Use this version for your needs.
The optimizations of v. 2.0 are discussed in this article in Oracle's Java Magazine