For those of you who thought shapeshifter was so great because it doesn't modify System files... you are wrong. Look at what I found. I installed the theme Siro with ShapeShifter 2.2 and it does modify the Search.bundle file for Spotlight. Just look inside the package contents and you'll see the files from the theme you have installed.

So that whole "ShapeShifter doesn't touch your System files" thing is incorrect now.