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But the signals are changing depending on ext_clk that is about 100 times slower than the original clock and these signals are resynchronized by a fifo between the Quartus design and the Qsys system. It's not enough to say they are static?
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If you are reading the data via the USB JTAG interface then, the read interface is the limiting factor. So your signals are dynamic, and need to be captured into RAM, and then that RAM can be read out over USB.
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And a "no matter" question: what is (is there) the command I have to use in Quartus to list the content of the working directory? I tried 'ls' and 'dir' but it won't work.
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The Quartus console is a Tcl console, you can use Tcl commands.
Cheers,
Dave