ExtUtils::MakeMaker is a good way to go ( god knows shell scripts aren't too portable ), and is practically guaranteed to work on any platform perl runs on.

You should look at least look at Apache::Config (there's a whole bunch of those modules, and you ought to at least consider two of those).

Another way to go, and potentially easier to manage, is Ant (it's all xml), which is practically guaranteed to run on any platform java runs on.

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** The Third rule of perl club is a statement of fact: pod is sexy.