I am considering to use the Dobot arm for a feasibility study, I will need to make use of open-dobot to that end, my question is: The arm that I presently have access to is "Dobot Magician". Is the Magician version HW compatible with the "Dobot v1"? I mean as far as Arduino board as well as the FPGA board?
No, it's not. But you can replace electronics (it's one board) with RAMPS. Accelerometers is a different story. I'm planning to add support for those MP65 weird accelerometers in couple of months if no one else does that before then (I simply don't have time now).
you replied that they were not identical, "but you can replace electronics (it's one board) with RAMPS"; are you referring to the FPGA board that is replaced with RAMPS 3D printer controller? This is then no different for the Dobot magician and the Dobot V1?