Cool game, but can I suggest a thing or two?
Having corruption permanently remove branches of the tree of humanity with no stated way of regaining them feels rather punishing, and you could even potentially lose your serial number. What if you had a factory reset type command? Sure, you'd lose all gained strands, but I think it might be a welcome trade-off if you get to a point where you've corroded your tree beyond repair.
I also think that the definition of protocols should be more like a programmer's method, which contains the name of the method, and the parameters. it would allow for slightly more complex protocols that can also focus on multiple things, or even allow for mechanisms that could repair one's self. Or heck, even an ignore(protocol) protocol to prevent loops without needing to break free. More interestingly, one use I thought of is sharing a protocol to another angel if it's useful enough. I also don't see a stated limit on protocols.