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$ perl -MJSON -le '$output=`./asdf`; print encode_json([$output])'
output to stderr
["output to stdout\n"]
$ perl -MJSON -le '$output=`./asdf 2>&1`; print encode_json([$output])
+'
["output to stdout\noutput to stderr\n"]

$ perl -MData::Dumper -le '$output=`./asdf`;print Dumper $output'
output to stderr
$VAR1 = 'output to stdout
...
output to stderr
';