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I have to agree. I think you could move the entire Links section into a plugin that people can install if they need it. I've only used it on one site ever, so I'd bet most sites won't miss this too much. It would be nice if someone took this on and improved the future Links plugin to add features, etc. You'd get the best of both worlds then.
3 years ago on Should Blogroll "Links" be removed in favor of WordPress Menus?