It sounds to me like you have a good use-case for Pinto. Jeffrey Thalhammer spoke to the Los Angeles Perl Mongers last week, presenting Pinto and giving some excellent examples of how to use it effectively. I expected to find his slides on the LA-PM website but they're not up yet. You might get in touch with him to request the slides. On CPAN he is thaljef and on Github, thaljef.
Pinto can be integrated with a DarkPan repository, and it also can be placed under version control (git or svn depending on your preferences). It allows you to pin certain modules to a specific version number, while allowing others to be upgraded. It allows you to maintain local (darkpan) versions of modules, and other dependencies not included in your local repository will still be grabbed from CPAN. It seems very well thought out. I'm anxious to find the time to give it a try myself.
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