Depending on whether you want to do monkeypatching or real source patching (both of which can be confusing depending on whether you change/increase $VERSION or not), you might find the idea of the Distroprefs in CPAN interesting. The distroprefs allow local setting of preferences and (more to the point) automatic application of local patches, which hopefully apply cleanly across more than one version.

In reply to Re: Maintaining Local CPAN Patches by Corion
in thread Maintaining Local CPAN Patches by Ovid

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