Basically the set of dependencies is (or should be) a directed acyclic graph. One does what's called a "topological sort" to determine the proper ordering of the nodes (it's nothing more than a post-ordering in a depth-first traversal). Take a look at Algorithm::Dependency.

A standard approach to represent dependencies is to do list the "target" followed by all the items it directoy depends on. E.g.

myapp foo.o bar.o baz.o
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Both A::D and make use this basic idea.