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Currently (Eclipse 2.0), entries under each node inside the Preference page are alphabetically ordered, when in most cases, it makes much more sense for the end users to see them arranged and clustered together in some functional order. The lack of support for programmatically arranging these entries make it time consuming for users to find what they need.
I am goinmg to mark this as a duplicate of Bug 36965 and move your comment there so that you can generally follow what we are doing for the preference work for 3.0. *** This bug has been marked as a duplicate of 36965 ***