Simplify Vertices and Edges collections, remove unneeded factory methods and favor collections over simple arrays

[clue]

// old
$vertices = Vertices::factory($arrayOfVertices);
$vertices->getVerticesIntersection($arrayOfVertices);

// new (already supported before)
$vertices = new Vertices($arrayOfVertices);
$vertices->getVerticesIntersection(new Vertices($arrayOfVertices));