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Is there a way to see the percentage of documented code and see what parts are not covered?
Interesting idea, didn't think of this. Will mark it as feature request for the moment to have it in idea pool for future.
As for the second part - appledoc should spit out every undocumented object. If you don't get that output, check if you have --no-warn-undocumented-objects and/or --no-warn-undocumented-members cmd line switches somewhere (may be in your global or project settings files besides cmd line).
I integrated the undocumented output into my continous integration flow with Jenkins, so I get a nice clickable report. For now it's good enough.