Change marker bits to avoid a ctrl-C triggering action
Use Leonardo D0 & D1 pins for Serial

Instead of using the SoftwareSerial I now use the hardware serial pins
D0 & D1 with the Serial1 class.
Emit what function is ready

It gets confusing otherwise if some key gets pressed mistakenly and an
unknown function is started.
Handle programming timeouts better

Exit with an error if we reached a timeout for some reason.