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@files = split /\s*,\s*/, $config->{path}{files};

foreach my $Section (values %$config) {
 # $Section is a hash ref containing the values of the section, not th
...
    $Section->{$value} = [split /\s*,\s*/, $Section->{$value}];
  }
}

 foreach my $value (qw(files colors and other options that should be 
+arrays)) {