I just found out a newt trick when using Ubuntu to access some hidden document folders on your iPad device when using Ubuntu. By default, when you connect your iPad to your Ubuntu machine, you'll get 2 new mount points: one for the DCIM content and another for the shared Document folders for each app. But not all apps have their Document folder shared by default so you only see those that have implemented that feature.
If you open a console and move to the ~/.gvfs folder. You will see the 2 mount points, one of them related to the shared document folders. For example, mine shows up as ~/.gvfs/Patrick Ipad Document.
If you list the content of that mount point, you'll see a bunch of folders, one for each app. For example, for Minecraft PE, it will be listed as com.mojang.minecraftpe. This is an empty folder but only the name is important...
Once you have found the app that you want to access, move out of the mount point and disconnect the iPad. The reason is that you need to disconnect the device for further steps to work properly. Otherwise, Ubuntu will report an error accessing the device.
Then reconnect your iPad. In Nautilus, access the "regular" document folders as usual. When you see the list of all the apps, press "Control-L" and you will see a strange URL looking like this: afc:/1231sdfsdf12323sdfsdf.3/. This is the root of the iPad (kind of). At the end, add the folder name of the app that you want to access even if it's not available in the shared document folders.
And you're in! Drill down in the sub-folders as needed. With the Minecraft PE example, you can access your maps or even add new ones. I did the same with iDOS ( I was lucky enough to still have it in my purchases even if it's not available in the appstore anymore) and was able to install Windows 3.1 in it...
This was done on an iPad 1, with iOS 5.1 no jailbreak required... And Ubuntu 12.04 with the default iDevice libraries.
Be careful not to break anything