I think you misunderstand. Bioperl consists of 10's in not hundreds of modules, as new modules are developed they are simply added to the growing list of modules available under a single CPAN package. This makes it difficult for a third party to reuse Bioperl code in their own scripts/applications as it would require the whole Bioperl package to be installed as a prerequisite. Therefore the devs are looking to split up Bioperl into smaller chunks with dependencies correctly setup between these smaller chunks. Therefore if someone wants to be able to read/write sequence files from their own script, they will then only need to depend on a smaller subset of the Bioperl modules i.e. Bio::SeqIO::*

The question is, how small can these chunks be? Is there any limitation or is it simply a maintainence issue for the devs if they split things up too much?

After the split, several bundles could be made to organise the smaller subsets of modules into larger bundles with similar functions.