my $input_file = undef;
...
my @files = undef;

These are examples of types of statements that I see in several places in your code and that I consider programming tics that should be addressed with psychotherapy or powerful behavior modifying drugs.

The first,
    my $input_file = undef;
defines a lexical scalar variable that is default-initialized to undef — and then explicitly initializes the variable to undef. I see no point to the explicit initialization, but it can do no harm.

The second type of statement,
    my @files = undef;
can potentially do some damage because it doesn't do what I think you think it does. A lexical array is defined in an empty state by default, but this statement explicitly initializes the array with a single undef element.

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my @files = undef;
 ;;
 dd \@files;
 ;;
 print 'number of elements in array: ', scalar(@files);
"
[undef]

number of elements in array: 1
[download]

Is this what you expect and want? I thought not. In the example code you posted, this semantic error, by good fortune, does no harm (that I can see), but it is the kind of error that can bite you in the ass at any time given the opportunity.

Update: If you want to go the explicit useless initialization route for list-type variables, the correct syntax is
    my @array = ();
    my %hash  = ();
but again, these statements | initializations would IMHO just be more evidence of a need for medical intervention. The only circumstance I can see in which such statements | initializations can barely be justified is when an initial empty state is vital to the correct operation of a succeeding algorithm and you don't want to bother emphasizing this fact by going to all the trouble of typing a comment.

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