There are a few apps with highly confusing version numbers. For example, Expect <http://expect.nist.gov/> has a released 5.44.0 and 5.44.1, but they are "recalled": 5.43.0 is the actual latest version (as used by Linux-From-Scratch dev. version, for example). And there have been worse offenders on occasion, for example Adium (luckily OSX-only; see http://en.wikipedia.org/wiki/Adium for the horrendous history). I think it might be beneficial to provide a way to override the default version-ordering. Also there are some apps that are renamed while being the same thing, such as gaim->pidgin or ethereal->wireshark... but those usually don't cause any real trouble. It's more the above situations, or other non-renamings like Qt(3 vs. 4) that cause trouble...
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