Well....they *are* all in one file. But @ISA should be local to each package's namespace. Not that I'm sure what effect it has (if any), but I also have brackets around each package & its code, ala:

{package one;....}
{package two; @ISA = qw(one); use base qw(one);...}
{package three; @ISA = qw(two); use base qw(two);...}
{package four; @ISA = qw(three); use base qw(three);...}
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I have other duplicate named, but in different package variables too. I think each @ISA is specific / package -- otherwise how can you walk the symbol table for a package to see if it ISAnother type package?