Choose a .sm file (.sm.old is fine too), open it in a text editor such as Notepad, and paste the entire thing into the big textbox. Then click "super shuffle" and it will generate a new file with everything shuffled around. Only the first chart in the file will be shuffled (if you want to shuffle a different chart, clear the ones before it).
"Rigidity" is a very important number. A higher rigidity means that the patterns are closer to the original (but then there is less flexibility for their placement). Specifically, rigidity equals the number of chords back that the program will check. So if you set it to 0, it's the same as the Super Shuffle in Stepmania - notes are individually shuffled. If you set it to 1, all 2-note sequences will have the same structure as in your file, so jacks stay jacks and stream stays stream. If you set it to 2, 3-note sequences have the same structure - jacks stay jacks, stream stays stream, minitrills stay minitrills. And so on.