Merge doc/sphinx/references.bib into doc/references.bib

File sphinx/references.bib was not used, and was messey. I merged it
into doc/references.bib. Also I fixed a collision between two duplicates
of Luding2008.

Still there are hundreds of undefined references during compilation like:
  LaTeX Warning: Hyper reference `yade.utils:yade.utils.createInteraction'
  on page 112 undefined on input line 6806.
but that seems unrelated.