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After some more experiments my conclusion is that exec works if system-console is hosted in a bash shell, and not if it's hosted by a native windows shell or windows process (such as Quartus).
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Ok. That was what I was thinking too, however, the comments on the link I posted made me think otherwise.
So the question then becomes, how can you select the shell? I suspect the answer is that the shell is fundamental to the process, since when you launch the application, it inherits the shell. The solution might be to replace system-console with a bash script that starts system-console. That way when you execute system-console from a windows shell, you would actually be executing the script, which in turn executes bash, and then the real system-console application. With that setup, the shell should be bash.
Cheers,
Dave