Why not just call SUPER::new() at the end of your new() override after doing your filesystem stuff instead of returning? Then you do not have to worry about how the ORM happens to handle things.
In your specific example, why would you want to die if the directory exists? Just pass on and call SUPER::new(). Or spell it out as Class::DBI::new(), if you are using multiple bases.
Stay out of its way instead?
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