After upgrading to firmware v2.1, I used quickpwn to re-jailbreak, and the first time I started Cydia it moved everything (wish it asked about that - wish it didn't use random names - etc).

In any case, I just discovered that since I did an upgrade, the previous (2.0.x) relocated directories already existed under /var/stash, so I had two copies of /Applications, /Ringtones, /Themes, /Wallpaper, etc.

Seems like a good way to waste space instead of saving it.