in reply to
code-controlled module naming conventions?
You might have a look over at the bioperl bulleting boards. There is a very active discussion on refactoring bioperl using Moose as the newer development framework. Given that you are working with mass spec data, there is obvious overlap in how use/call your modules and what the openbio crews typically do. I think being compatible with the module handling conventions in bioperl would help adoption of your modules once you release them into the main stream.
yet another biologist hacking perl....