i was reading about people upgrading their phones to 2.0.2 and losing their 3rd party apps (ones installed from installer and cydia) becasue they are in the root partition.. now is there any reason why installer and cydia cant install apps to the same location the app store saves its apps, which would then allow them to survive the upgrade process

there is prob an obvious reason why this cant be done, but what is it?

Cheers