Using the latest source, the following header file raises an exception because STGNumberSign is already registered somehow.
It throws this even when parsing just this header file in isolation.
I copied the file into my testing project and it does not throw any exception. It just warns about the STGNumberSign not being documented.
Appledoc does not scan files based on your project. It scans all files in the given directory and subdirectories. My guess is that you have a duplicate file somewhere in your folder structure.
Yes I know it only scans the directory, but that file alone in its own directory still throws for me.
Here's the AppledocSettings.plist I'm using: http://pastebin.com/kvjAAbxB
So, to make my repro steps totally clear:
Previous reply deleted. Remove the -input section from your plist, or do not include the '.' on the command line.
You are basically processing the same folder twice.