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Bookmarks go out of date because the "book" is always changing. A smarter way to make a bookmark would be to base it off a method. If the file has changed since the bookmark was made then you could default to the top of the method the bookmark was in or you could use the top of the method as the point relative - so the bookmark would be 10 lines down from the top of method X in file Y. - to the bookmark and if the method disappears the bookmark should too.
Moving to JDT/Text.