Yes, creating rational directory structure for our application is our primary goal. We want to put things in a standard place, so people that understand the standards, understand our application setup. We also want to structure our directory tree to facilitate building standard packages so people can install our software one their own servers.
Thank you SilasTheMonk and jakobi, I now realize that we don't want to publish a cpan module. We have .pm files but none of them are of interest outside our application.
The docuument we want is Debian (draft) webapp manual