#!/usr/bin/perl
use strict;
use warnings;
use Data::Dump qw(pp);
$|=1;  #turn off buffering to stdout for debugging

my %HoH;  #{extension}{name}

while (my $full_name = <DATA>)
{
    next if $full_name =~ /^\./; # skip names beginning with dot
    my ($name, $ext) = $full_name =~ /([\w.]+)\.(\w+)$/;
    next unless defined $ext;    # skip bare names wihout .extension
    
    $HoH{$ext}{$name}=1;
}

pp \%HoH;

foreach my $pdf_file (keys %{$HoH{pdf}})
{
    if (exists $HoH{epub}{$pdf_file})
    {
       print "do something with $pdf_file.pdf and $pdf_file.epub\n";
    }
}

=prints
{
  doc  => { baz => 1 },
  epub => { bar => 1, baz => 1, boo => 1 },
  pdf  => { baz => 1 },
  txt  => { "baz" => 1, "boo" => 1, "some.long.name" => 1 },
}
do something with baz.pdf and baz.epub
=cut

__DATA__
.
..
some.long.name.txt
baz.txt
baz.epub
baz.doc
baz.pdf
bar.epub
boo.epub
boo.txt
barefile