I really don't think modifying CPAN code is good practise, unless it's to fix a serious bug that you then give back to the author.
If I really want to modify the behaviour of a CPAN module and it's not reasonable to subclass (or I couldn't be bothered ;) I usually inject my own subs/methods into the namespace from my own code. That way you don't need to carry around modified CPAN modules. And with any luck, minor upgrades to the cpan module won't break your addins (which are hopefully based on documented API anyway).
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