So what you're saying is:

1. Program A outputs data with "\n" at the end.
2. Program B chonks the data.
3. Program A fails in some way, and outputs a line without a terminating "\n"
4. Program B dies and reports the problem?

This will appear in test as.. what? a failure in Program A or Program B?

If Program A outputing "\n" at the end of the line is such a cruicial matter, shouldn't you be testing Program A's output explicitly for "\n" (or whatever your seperator is) instead of condeming the use of chomp everywhere?

And by using chop, how do you catch this in testing? like so?

$data = get_input_from_program_a();
$chopped = chop($data);
if ($chopped ne $/) {
   die "Program A is acting up";
}
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I'm just not up to the level to think that deeply into your problem, maybe you can help me understand?