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If one creates a project in windows netbeans 6.9 and then the same project gets opened in linux netbeans 6.9 there is a Resolve reference problems error message. The same happens for vise-versa. There is no real problem since project can clean and build there's just this message that should not be there. The reference issus is for javaws.jar and plugin.jar.
Already fixed. Thanks for report. *** This bug has been marked as a duplicate of bug 187673 ***