Move Graph::Base to Graph

* removed the unused Graph::Collection class
  (Graph now uses 1 Fact::Collection, that stores
   both facts and provenance_facts)
* later the graph collection may be readded when
  we really need to store multiple files
  (but probably YAGNI by then ...)
* this further cleans up to public API (as
  seen in YARD):
  graph = Graph.new
  graph.store_fact_set # TBD
  graph.to_CSV
  graph.from_CSV(IO) # TBD