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Is there a command to search the ENTIRE design (all .vhd files and Megawizard functions) for a certain signal?
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Assuming you've gone through synthesis, go to View -> Utility Windows -> Node Finder and search on Design Entry(All Names).
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grep, it gets installed with Nios II EDS (run Nios II Command Shell, cd /cygdrive/<drive_letter>/<path>/<to>/<project>)
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Not part of Quartus, but ultra edit allows you to do exactly what you want.
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I tried the node finder but nothing pops up. It seems to be unresponsive

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