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I imagine one method would be to do something useless with spare gates in a design. Like tap out the authors name in morse code, or '(C) A-maze-ing FPGA desgins Ltd' in ASCII and have it output on a pin that isnt external to the package you are using.
What level of reverse engineering are you hoping to prevent, or are you just trying to prevent use of the binary?
Watermarking images is much easier becuase they are almost always noisey to start with and plenty of mathmatics are avilable that can provide rotation/translation/format invariant information. FPGA binaries have unused gate data, but if you fill this with data not related to the circuit pretty soon you end up with a non deterministic FPGA.
I suppose more simply and perhaps more cryptographically useful, you could set values in the cell lookup matrices that wernt actually used by anything, and some manufacturers like xilinx are willing to provide enough of the binary format for this information to be retrieved. Youd have to work this out for every specific device you wanted to protect.
I think we need more information. Are you trying to protect a single device, or produce a generic product and what level of reverse engineering are you trying to protect it from?
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