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Have you taken a look any at the FreeBSD ports system? It uses makefiles to manage pretty much any software install you can think of. Additionally, there's a pretty good infrastructure there for managing custom build trees, etc. Additionally, they also have things like BSDpan that let you use arbitrary Perl modules with the package management system.

I've used ports, but I've never developed a project using it, so maybe I should try that out. But "uses makefiles" does not make me particularly optimistic for its pleasantness. I really prefer (and think it's been proven possible to build) declarative, rather than imperative, systems for managing dependencies.

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