If the SQL::Library isn't for CPAN, then it is more of an layer of the app above the CPAN modules used (or currently being refactored out from old code).

Can you think/structure app + SQL::Library as a kind of 'user' providing code or code refs for use in hook functions provided by lower level modules? Alternatively, with similar effect: can you think of this as sub-classing the cpan modules?

If I correctly see the issue, shouldn't such an approach solve at least the 'future CPAN module depending on external files not in CPAN'?

hth,
Peter

ps: if you've split the modules in one for CPAN, one for internal use and both are installing in @INC following CPAN guidelines, why do you need an explicit search of @INC? Unless for instance-specific templates. And that would be application-instance-specific app-configuration, and not use Perl's @INC at all.