Since a lot of users will be inputting a mono signal most of the time, here's a suggestion for an alternate function for input 2.: Could it be used for pitch detection, (but with effects only being applied to the signal coming into input 1)? A user could send a dry guitar sound (by tapping some signal early in the signal chain, before distortion) into input 2. This signal would be used for consistent pitch detection only. A dry signal should be preferable for pitch detection purposes to an effected one. Wouldn't this improve the harmonizer tracking for heavily distorted guitar or synth sounds?
