I realize that I lost some disk space after I updated from 3.0 to 3.0.1 and rejailbroke.
I expected all the Cydia apps to be wiped out by the firmware update and the associated disk space be freed up.
However, my free disk space remained the same after rejailbreaking.

So, I logged in via SSH to do some investigation.
I see that /Applications is now pointing to /Applications.<some_random_characters>; it was pointing to /var/stash/Applications.pwn.
And surprisingly, the original Applications.pwn is still there.
Not only the old Applications is there, all other directories that are under /var/stash (e.g. Ringtones, Wallpapers, include, libexec, etc) have two instances as well.

I tried to move some Cydia apps from the original Application.pwn directory to the new one and they open up fine and even remember my previous settings.
I don't know if the apps works 100% though since I think some required files in other directories (e.g. /System) may not be there.
Also, Cydia doesn't know the relocated apps exist, so they don't show up in Cydia, which mean I won't get any updates notifications.
So, I think this may not be a good idea for backing up Cydia apps for firmware update.

To move on, I can just re-install all my Cydia apps manually and removed the old Applications.pwn and all other old directories. But I just want to see if anyone knows if this is normal or what steps should be taken when rejailbreaking in order to avoid getting those duplicate directories.