DirPatcher

This tool can interest you, if you want to copy files from a folder to another and keep a save of the overwrit ones.
The tool just need a source folder, a destination folder and a diff folder (where save files will be stored).

You can also use a "revert" functionnality to revert all modifications, using the diff folder :)

This tool can also be used with normal interface or by command-line.
ex: java -jar dirpatcher-1.0.jar source target diff
java -jar dirpatcher-1.0.jar -revert diff target