What I could not understand is in /lib we have modified modules and in
CPAN a copy of the 'original' (stock)  system CPAN, is that correct?

I think this might be true for Audio::Scan (only). But not in general. Modules we modified are supposed to be in /lib, sotck in CPAN.

If /CPAN is different than the system CPAN is by accident, it should
never be and it must not be because a LMS specific feature, is that
correct?

I don't understand your question.

What if we want to have a modified module (that should in /lib) BUT only
for a specific arch or PERL version?

That would be a mess. Is that in the context of a plugin? You can provide your own modules in a plugin, but I'm not sure whether it would be possible to override the LMS' modules.

--

Michael
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