I'd go with
dws on this one, $/ is a nice thing to be localizing, and often.
On the other hand, there are a couple of other approaches that are possible in this case. The first is to use my super-friend, the transliteration operator:
$file =~ tr/\r//d;
The other idea that comes to mind is a more complicated regex as an argument to split. I don't see this used often, which is a pity:
my @lines = split(/(?:\r?\n){2,}/, $file);
Take these with a grain of salt, because they could require some tweaking depending on your circumstances. Just remember that hammers in Perl usually have GPS and homing as well.
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