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Cons: Need to extract a reference to work on and save it back to the file.

Whatever solution you use its going to involve refereneces, so that can't be a con, since it's a given

Also, you don't have to work with references if you use Data::Alias

Is this good, bad, and/or ugly ?

Um, poop :)

Some links you might look at

update: supposedly better than MLDB is DBM::Deep - A pure perl multi-level hash/array DBM that supports transactions

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