You should change:

            chomp $_;

            # Split the line by whitespace
            my @array = split (/\s+/, $_);

            # If the first column of a line is blank whitespace, shift
+ it out so the
            # first column corresponds to actual user viewable data, w
+hich is the way
            # a user will count the columns, ignoring leading whitespa
+ce.
            if ($array[0] eq "") {
                shift (@array)
            }
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To:

            # Split the line by whitespace
            my @array = split;
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Because split with no arguments ignores leading whitespace so there is nothing to remove and it also removes all trailing whitespace so there is nothing for chomp to remove.

            while (<@array>) {
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That is short for:

            while (glob join $", @array) {
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and it is usually written as:

            foreach (@array) {
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