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I have created a possible fix for Issue #5
It turns out the problem is not caused by the XML doclet, but by inconsistent processing by JavaDoc itself. If you give JD an explicit file to work with, it parses and processes the inner classes at the top level, and then again as contained elements of the outer class. If you give it a package, it only processes the inner classes as contained elements. Hence, if you add class processing to the outer class parsing, it generates two copies in some cases. To solve this, I am maintaining a keyed list of classes, within each package, by qualified name. This list refuses duplicates.