I want to eliminate all user data on the phone except for apps + data and my camera roll. This isn't exactly easy as far as I can tell...
So you mean like, restoring from a backup... except, without the backup part?
Then yeah, do as I say, copy the entire folder but then copy back the documents folder manually for each app.
You can make some sort of list on terminal (via iDevice or SSH) so that you know what encrypted folder corresponds to what app later on.
You could automatize the process with a script that would take the old filename, match with the new one and then copy the settings to the new folders.
Imma make something like that but it will take me time (in order to manually sync iPad and iPhone for stuff that is not iCloud-enabled).
The camera roll, well, my advice would be avoid the hassle and just sync the photos to the PC (app, photo stream, iTunes, photosharing site that won't compress your pics, you name it) then sync back.
About apps as such... well you can see inside each encrypted app folder there is a .app folder. You can add those to iTunes but then it's a hassle since you'll have icon-less apps and I'm not sure the payload would persist (the information on each app where it says you're the buyer), so no updates anymore on iTunes and the like.
You can inject the icon back on, but I'm not sure about the payload data.
But why would you do this? If you already have them on iTunes, then sync them back, then afterwards manually (or automatically with a script you made, as I explained before) copy the app data.
