Just to nitpick a tiny bit, I want to warn about your modification to $/.

By doing things the way to did, you are setting yourself up for crazy-ass bugs. You properly localize the variable, but the scope of the localization is way too broad.

I suggest getting in the habit of anonymous blocks every time you localize a global variable. Like This:

open OUT, ">fixed" or die "Couldn't open fixed: $!";
open IN, "<junk" or die "Couldn't open junk: $!";
{
    local $/ = undef;
    ($_ = <IN>) =~ s/\n{2,}/\n/g;
    print OUT;
}
close IN;
close OUT;
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This way you properly limit the scope of local $/ to just the lines you need it. And wont accidentilly screw yourself up later.