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open SH, "| /bin/sh" or die "can't launch subshell: $!";
for my $file ( @files ) {
...
    print SH $cmd; # stderr from subshell will go to STDERR
}
close SH;

 $ run-em-all.pl > log 2> errlog

    $cmd = "echo running $file 1>&2; perl -Ilib $file"
    print SH $cmd;