Empty Directories in ~/Library/Mobile Documents I'm browsing the directory in ~/Library/Mobile Documents running the latest version of Mountain Lion and I see may empty folders that correspond to applications that I have used in the past, but whose iCloud data I don't necessarily care about (some shouldn't even have iCloud data).

Additionally, looking at the Manage Storge section of iCloud settings on my iPhone, there are only 3 or 4 apps listed in iOS, so it seems these folders that are empty on my mac could be safely deleted. Is this the case? I don't want to delete these folders if someone can't confirm that its safe to do so, because I don't trust iCloud to do the logical thing in this situation, which would be happily accept the fact that I deleted these empty  folders.

Curiously, I have some applications that I know are syncing through iCloud, because I have the same data on my iPhone and my iPad, but don't have corresponding folders in ~/Library/Mobile Documents on my Mac. Do some iOS applications store their data in a different location?

None of this seems logical, so can anyone make sense of this and provide some insight into what iCloud is doing behind the scenes here?
~/Library/Mobile Documents is basically a mapped network location(to iCloud) and allows you to interact with the documents created by certain apps(default location) most likely they are left over from poor un-installers not cleaning up after themselves or left intact on purpose incase you decide to re-install at some point.

I would contend that it is safe to delete if you don't plan on using those applications, and also assuming if they are generated by an application that when they are needed they will regenerate themselves as needed. Make a copy of them and put them on your desktop and delete them to see what happens. If it breaks copy them back.

On a side note, are you doing this just to keep things clean? Are you in this directory through finder enough that these folders slow your navigation down? I appreciate wanting to keep things clean, however their existence probably won't slow down any indexing by spotlight, use any bandwidth by iCloud or take up a significant amount of HDD space.