what should they be doing (from the perspective of a module author) when they perceive a need to amend a core module

My two cents, At a minimum, make sure any thing that dies/carps mentions that it's a patched version of the module and bump/alter the version number. Better would be to get the patch taken upstream -- or, in this case, perhaps, get File::Path pulled out as a dual core/CPAN module so the patch could be made generally available in the "latest" release of the module on CPAN.