my %hash;
my $flag = ".flag";

foreach my $file(@files) {
    if ($file !~ /\Q$flag$/) {           
        print "$file\n";          
        $hash{$file} = 0;
    }
    else{
        my ($short = $file) =~ s!$flag$!!;
        $hash{$short}++;
    }
}

%hash = map{ $_ => $_ . $flag }grep{ $hash{$_} }keys %hash;