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When setting super class name to some public static inner class, just a short name is used instead of outer-class.inner-class. Generated code is not compilable.
Created attachment 841 [details] junit test
As I understand the test source, you have some existing inner class coded as public class OuterClass { public class InnerClass { } } then theInnerClassElement.getName() has sourceName property = "InnerClass", and its fullName property should be set to "whatever.package.OuterClass.InnerClass". The superclass property is just an identifier, nothing more - you, as the caller, are responsible for translating the name into appropriate target context (e.g. prefix it with outerclass/package). If you want to be sure, the best is maybe create Identifier from the inner class' full name.
Resolved for 3.3.x or earlier, no new info since then -> closing.
Resolved for 3.4.x or earlier, no new info since then -> closing.