use warnings;
use strict;
use File::Basename;
use File::Copy;

my $dir = 'ParticleAcquisitionDataImages/'; # or whatever
my @files = glob "${dir}*.jpg";

my $rename_index = 1;

for my $file ( sort @files ){
    next if -d $file;
    my($filename, $directory, $suffix) = fileparse($file, '.jpg');
    next unless -e "${dir}$filename.xml";
    $filename = changename($filename);
    open my $fh, '<', "${dir}$filename.xml" or die "$!";
    seek($fh, 498, 0);
    my $newdir;
    read($fh, $newdir, 3);
    close $fh;
    substr $newdir, 1, 1, ''; 
    mkdir "$dir$newdir" unless -e "$dir$newdir";
    for my $ext ( qw/.jpg .xml/) {
        move "$dir$filename$ext", "$dir$newdir/$filename$ext" or die $!;
    }
}

sub changename {
    my $filename = shift;
    for my $suffix ( qw/.jpg .xml/) {
        rename "$dir$filename$suffix", "$dir$rename_index$suffix" or die $!;
    }
    return $rename_index++;
}