When I have a situation like this, I will just isolate all of the configuration-related code into a single perl module or require file, and then maintain those two files seperately from the rest of the code. When I sync versions between development and production machines, I just don't include that file. That means I have to update it by hand if new variables are added, but if you keep the number of configurable things small you don't have to modify it very often anyways.
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