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Simulation might be a good first step in order to prove first correct functionality
but what if there are
some components which cannot be reproduced my models so
easily?
Inside the FPGA, don't use vendor core generators. Write your own code that infers what you need.
For memory and other external parts, choose devices with free models or write some code. You may not need a very fancy external model to verify your own synth code.
Once you're done, you can "probe" wherever you like with sim waveforms, and have the freedom to make changes fearlessly.
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