There's more to large-scale programming than just the smart management of modules and packages.
I agree, and it seems to be to be a hard thing to find good books on. When I was looking around about a year ago, all I was able to find was a lot of research papers online.
I wouldn't hesitate to recommend the Alpaca book for the areas it covers, but it wouldn't be the only source to use in this particular case.
I am not familiar with the "Alpaca" book, can you elaborate? And any other suggestions you have would be most appreciated. They don't need to be specifically about perl either, I know several other langauges as well, and I am also interested in theory/best-practices/concepts/etc.