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The usage "A is augmented by B" indicates that B is the implied subject in the passive-voice construction "A is augmented". That is, B is doing the augmentation: "B augments A".

The usage "A is augmented with B" implies that B is what A is augmented with, by an unspecified subject. This is a predicate adjective verb phrase.

Thus, one could write "The fruit salad is augmented with papaya by Sofia", meaning "Sofia augments the fruit salad with papaya".