How can you possibly have hundreds of run modes (are they really tiny? how are they related? Can you draw me a picture? -- outline the app, it's functionality, the modules it uses, the enviroment it runs in .... a picture)?
Has it dawned on you to split this application up into 3-4-20 different applications?
CGI::Application will LOAD EVERY MODULE YOU USE, as would any other perl program if you use all of them. The alternative to useing a module, is requireing it (perldoc -f require), or simply eval-ing the use statement (perldoc -f use).
Any thoughts and recommendations to handling such a situation?
Yes, use strict, use warnings, use mod_perl, and don't worry about it (or, restructure your app -- can't really suggest how cause I don't have a picture).
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