You have an infinite loop:

while (%stuff_to_store) { #see if it worked by printing out each eleme
+nt of hash stuff_to_store
                    print; #its not working and I don't know why
                }
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You probably want to iterate over the hash thus:

while (my ($k,$v)= each %stuff_to_store) { #see if it worked by printi
+ng out each element of hash stuff_to_store
                    print $_, $v; #its not working and I don't know wh
+y
                }
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But you probably have only one value in the hash. Why the hash ?

I'm guessing you want a multi-level hash of hash of Array, but perhaps that may be too complicated. If you understand this code, feel free to use it, or ask!:

  push @{ $stuff_to_store{$dir_to_process}{$file} }, $_;

  # Debug print it..
  for ( @{ $stuff_to_store{$dir_to_process}{$file} } ){
    print;
  }
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