Review of the improved bundle closure algorithm.

[NicolasRouquette]

See: https://github.com/JPL-IMCE/gov.nasa.jpl.imce.ontologies.tools/blob/861e95f779394dbfaabdcc04b149c6c076fa4b73/lib/BundleClosure/lib/graph.rb

def merge_vertices(s)
    new_vertex = Union.new(s.inject(Set.new) { |m, o| m = m.union(o.classes) })

    g = RGL::DirectedAdjacencyGraph.new
    edges.each do |edge|
      if s.include?(edge.target)
        g.add_edge(edge.source, new_vertex)
      elsif s.include?(edge.source)
        g.add_edge(new_vertex, edge.target)
      else
        g.add_edge(edge.source, edge.target)
      end
    end
    
    Graph.new(g.transitive_reduction)
  end

In the above, need to improve the checks to make sure that an edge is added if and only if
both edge.souce and edge.target are not in s