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For the pop-up displaying the files opened , accessible through the double arrows or CTRL+E in a workspace functional area, IN J2EE perspective, the list displayed would be more useful if would be alphabetical ordered.
Based on bug 463288 comment 0 this is as intended: "In 3.8, the order was: - group of bold entries for non-visible tabs, in alphabetic order - group of non-bold entries for visible tabs, in alphabetic order I'll restore the 3.8 behavior." Based on this, you should have two groups, both in alphabetic order, but that means that you have full alphabetic ordering only in case one of the groups is empty (only hidden tabs group = bold entries can be empty).