Update of bib file

Changed arXiv entries in bib and did some cleanup of the active entries based on last comment in [#567](https://github.com/stan-dev/stan/issues/567) (too large for me to do cleanup of old entries too). I have compiled the entire manual if you want me to e-mail it for review (2+ MB). An excerpt of the opening of the bibliography is below.

The missing portion of the old Bib file is restored, but the vast majority of that file is unused and should probably be pruned.

![bib opening](https://cloud.githubusercontent.com/assets/5596401/2671366/aa222d9a-c0d9-11e3-9774-bc46d3f5e426.png)