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[cli] Don't log to STDOUT if debug flags are set (#474)
It makes sense that error messages should be written to STDERR and all others should be written to STDOUT (as shown in #207). However, it would be convenient to parse the debugging output when the relevant flags are set. This change will disable logging to STDOUT and redirect all log messages to STDERR when any of the debug flags are set. (Resolves #473)
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