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EVALUATION
I am closing the issue for 7u releases. java.util.Arrays.useLegacyMergeSort property could be used in 7u releases to workaround the problem. Feel free to escalate the problem. In jdk8 we are going to fix the LayoutComparator class.
11-05-2012
WORK AROUND
java.util.Arrays.useLegacyMergeSort property could be used.
11-05-2012
EVALUATION
The risk to face the issue is not high, however the exception if it appears, prevents a user from working with UI.
The problem is tricky. We can't reject ROW_TOLERANCE, though with it there're examples of UI whose components can't be sorted to arrange a focus traversal order.
As a workaround I can suggest the following. In the Comparator.compare() method, mark components which participate in RAW_TOLERANCE relantion and set a rule that a component may participate in it only once. This will break long "ROW_TOLERANCE chains" (consisted of more than 2 components) into couples thus preserving transitivity.