The cpan client can be configured to apply local patches when it installs a module, preserving them across installations. I do not know whether cpanm or cpanp have this capability. Of course, the patches also have to be maintained, but that's only a problem if the module being patched is under active maintenance.

In reply to Re^2: editing of installed modules, a story of failure by Anonymous Monk
in thread editing of installed modules, a story of failure by gsd4me

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