[SignalTap-II] Signal colors Legend

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The reason why sometimes you end up with red nets in Signaltap is due to Quartus optimizations. The most common occurrence is a net that doesn't feed logic, Quartus will optimize those away. To avoid capturing nets that get optimized away when you are selecting signals to look at, make sure you use "Signaltap II: pre-synthesis" filter when locating the nets to capture. That should ensure the net is preserved and if it doesn't you can also use RTL attributes like "keep" to force Quartus to not optimize the net away.