1. Although it's not your problem, use strict;
2. Change @files = <IN>; to chomp(my @files = <IN>); - that will fix your problem.
3. A style note: Change for(@files) { to for my $line (@files) { and get rid of the next line. :-)

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We are the carpenters and bricklayers of the Information Age.

The idea is a little like C++ templates, except not quite so brain-meltingly complicated. -- TheDamian, Exegesis 6

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.