I remember previous versions of Perl working fine when reading <CR> terminated lines.
I'm a bit surprised. In my recollection, Perl is handling gracefully line endings for files prepared with the format of the OS on which Perl is running, but can't handle correctly cross-platform files. To tell the truth, I am very much used with these types of problems between Windows and Unix or Linux, much less with old Mac endings (especially nowadays).
I think that the while statement correctly splits the lines, but it is just the printing which goes over the same line again and again due to the carriage return without any line feed. Try this:
while (my $line = <$in>) { $line =~ s/[\r\n]+$//; print "$line\n";}
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