I faced this problem when I was revising modulemaker, the command-line utility that comes with ExtUtils::ModuleMaker. There are default values that come with the module; the user can save personal default values to a file which will override the original default values; and the user can then supply values via command-line options or the interactive mode.

It was quite challenging to figure it all out, and I haven't had to pay attention to it for several months, so I can't recite how it goes off the top of my head. But you're welcome to poke around in the source and see if it gives you some leads.