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.

![bib opening](https://cloud.githubusercontent.com/assets/5596401/2671192/a4df6fc0-c0d7-11e3-8472-61bb4c423715.png)