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Turns out both the Jumperless firmware was dropping characters from the commands because it wasn't waiting long enough between reading each character to the input buffer. Also jlctl was timing out because it wasn't waiting long enough.
But between the new firmware and this change, it's pretty rock solid.
Check it out
https://github.com/nilclass/jlctl/assets/20519442/b12b3518-45ae-4ce1-b05e-c913b243174f
I also added validation for the special functions on the Nano header, it still needs to somehow recognize them as actual rails and add them to the right special net, but at least it doesn't return HTTP BAD REQUEST and not update the rest of the connections in Jumperlab. There are a bunch of ways to fix that, but I'll let you decide what makes the most sense for jlctl.