The EMIS hybrid truck system uses an automatic transmission, but that's only because their system is computer controlled, using data pulled from the ODB2.
It just simply wouldn't be able to account for knowing what gear you are in and what the clutch is doing easily otherwise.
I figure that with a manual transmission, I can run just the electric while in neutral and other fun fuel economy tricks.
My big issue will be trying to figure out the best way to independently control the ICE and Electric throttles.
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