For your 1st warning message, I think you can just change:

  opendir(my $currentDirectory, my $pathToDirectory) || die "You sure 
+that exists, dummy?";
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to:

  opendir(my $currentDirectory, $pathToDirectory) || die "You sure tha
+t exists, dummy?";
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For your 2nd warning, this line is definitely the culprit, but I'm not sure what you're trying to do:

while ($boxEnd >= my $boxBegining, $boxBegining++) {
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Maybe...

while ($boxEnd >= $boxBegining) {
    $boxBegining++;
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