Möbius function for graphs??

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I'm reading this post and I'm getting a little confused. I am trying to find a useful notion of the Mobius function for directed graphs and have had little success in my search. I don't know much about graphs but I have done some enumerative combinatorics. So I guess my questions are:

  1. What graphs do they mean? Directed or undirected? With single edges or with multiple edges?
  2. What is the $M$ in that post? Is it the multiset of prime cycles (What is a prime cycle?)
  3. What is the Mobius function $\mu(M)$? Is it the same as the order theoretic Mobius function for the lattice of subsets of a multiset?
  4. Is there a reference for the Mobius function and Ihara zeta function result that they mention?