I'm running OS X 10.7.5 and have never paid any attention to saving documents on iCloud until now.
It appears that one application I wanted to use supports iCloud but the iCloud saving options are not available.
But then I went to TextEdit, which should have that option, but there is also no such option (no cloud icon in save dialogs).
I once turned off iCloud saving as a default with this terminal command:
defaults write NSGlobalDomain NSDocumentSaveNewDocumentsToCloud -bool false
But I didn't expect that to remove the choice to save on iCloud completely…
The documents & data option in iCloud system prefs is enabled. I tried disabling it, waiting a min, and re-enabling it, but no change.
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