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While I was correcting the XMI diffs for CWM 1.0, UML 1.3, and UML 1.4, I noticed that MDR explorer assumes that all uncontained objects in a MOF ModelPackage extent are instances of MofPackage. However, since MDR doesn't enforce the MOF constraint that every uncontained object must be a package, there are cases where non-package objects will be uncontained. For example, the symptoms of issue 25998 are not noticable in the MDR explorer in the "Model" view. Here is a patch that looks through all ModelElement instances to find the uncontained ones. However, this is noticably slower on large metamodels. See issue 26443 for a possible solution. With this patch, issues like #25998 become easy to diagnose.
Created attachment 7207 [details] Patch to search through ModelElement.refAllOfType()
I am closing all reports in category Java/Unsupported as wontfix. These should be dead issues --- if the reported cases are against some live part of the NetBeans IDE please reopen and we can discuss to which category they belong.