BTW in answer to your specific question, my personal answer is to use an application configuration module where each module says what variables it will import from its configuration scripts, but the configuration scripts are themselves kept in the same directory. Variables that need to be shared across multiple modules can be imported by the configuration scripts and then re-exported. A bit complex, but it works quite well for a system with ~60K lines of Perl.

This is essentaly what I'm doing. The Yaps::Config.pm reads in configuration data, creates several hashes, hash a couple of larges hashes itself, sets several flags (including debug flags), and global configuration data and exports it. All other parts of the application use this module to get at that data.