I hope I am wrong, but after installing iOS5.1 beta2, I see that the
app data of my phonegap app are now stored in the Library/Cache
See this screenshot my app data in iExplorer :
http://cl.ly/1p3L1U2W1J3y3I1T1r3y (before it was in Library/WebKit folder).
I will work right now on a backup of my users data on my own servers.
I have users using my apps since 2 years, and they have generated a
lot of data. It would be catastrophic if they loose everything. Hope
Apple will fix that. Maybe we should fill a bug report?