Nuked-MD-FPGA

The reality is that the vast majority of these FPGA-based clones don't actually perfectly emulate the logic. They're using the same reverse engineering techniques the traditional emulator developers used and sometimes even the same community documentation. The results are often quite good, but they're making a new implementation that matches the observed behavior of the original system to the best of their abilities. Now there are some exceptions. Nuked MD FPGA[0] is a recent example of an FPGA recreation that is a fairly direct translation of the original logic using silicon die analysis. In this case, the logic is basically identical, but as you guessed the physical layout is different. Generally speaking, you write FPGA "gateware" in a language like Verilog or VHDL. These don't intrinsically have any information about the physical layo

Kinda, sorta? This is like saying "a computer is not enough, you need a binary." What's here is the source code in Verilog. Once this is compiled by a Verilog toolchain, this produces a netlist (set of gates) which is synthesized into an actual bitstream (proprietary gate configuration file) for a specific FPGA hosted on a specific board. In this case, the project isn't very documented but it looks like fairly generic Verilog without a lot of vendor specific extensions. So, what you need is a Verilog toolchain which can synthesize the source code into a netlist, and then into a bitstream, and the right set of extra code to target an actual physical piece of hardware. Right now, it looks like the only board support that's checked into the repository is for the Icarus Verilog simulation environment: https://github.com/nukeykt/Nuked-MD-FPGA/