Dude! Further optimize! Let's see ...

    elsif (/\*{4}stuff\*{4}(.*?)\*{4}endstuff\*{4}/sg;
) {
        push(@stuff, $_);
        }
    }
[download]

That's one.

A style issue here:

for (my $i=0; $i < (@filenames); $i++) {

should be

for my $i (0 ... $#filenames) {
[download]

Now. If you're running out of memory, have you tried running it with a smaller dataset and figuring out where the memory threshold is? I can tell you it's not in loading your script into RAM ... it's just not big enough. It's when you're building these datastructures. Try just one filename's worth. If that breaks stuff, start making it smaller. Don't bite off more than you can chew! If it's not working, simplify until it does, then build it up again.

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/me wants to be the brightest bulb in the chandelier!

Vote paco for President!