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Minimum transaction output is (conservatively) calculated from the minimum relay fee setting. It did exist before, it was just set to '1 satoshi'.
We made 0-satoshi outputs non-standard a couple of releases ago, but consensus is that was a mistake-- 1-satoshi is not the right number, because the marginal cost of spending a 1-satoshi output is greater than its value.
Again, eventually it might be economical to spend 1-satoshi outputs. When it is, the minimum relay fee will be on the order of a satoshi or two, and this code will do the right thing.