Is it really so wrong and sinful to have a variable (mainly in a configuration package) to be used only once in the main code?
No, it's not wrong at all. Actually, it's more common than naught. Think of this message as the small price we pay to avoid spelling errors.
my $temp = $CONFIG::foo;
Unless you use $temp in more than one spot, you'll not avoid the message. Think about it.
This issue has been addressed a multitude of times. Check out this link and go from there. Good luck with it.
If things get any worse, I'll have to ask you to stop helping me.
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