There is no interface for writing to a file handle in IPC::Run, only appending to a scalar. This seems…weird.
Not sure what you mean here. This works fine: use IPC::Run qw(start run);
open(my $in, "<", "in.txt") or die "Err: $!";
open(my $out, ">", "out.txt") or die "Err: $!";
my @cat = '/bin/cat';
my $h = run \@cat, $in, $out;
close $in;
close $out;
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