[ondrasej]

As for commenting - code that is meant to be a library should have a clearly documented API. Perhaps not from the beginning, but as the API gets stable, the JavaDoc comments for generated documentation should be there. Though at the current state, tests and "getting started" examples (create a graph, list all nodes, determine if there is an edge from A to B, ...) would be sufficient (and would really help).

And since you're writing a graph library, there definitely should be a detailed commentary on the implementation of the graph (e.g. representation of the graph structure, memory complexity of the representation, and time complexity of common operations). Once you start working with larger graphs, using the correct representation and algorithms for your task makes a huge difference and it is something that must not be hidden from the users.