Api v2

New names and organization for version 2 of the opentree api.

These changes depend on some recent db structural changes introduced by taxomachine (already merged to master) which will necessitate a db update for oti. I have pushed an updated database to devapi and re-indexed the studies there as well.

@jar398, @jimallman, would you review this?  
> maybe we don't need this property now that curators can delete trees?

FWIW, the current curation app completely ignores the `is_deprecated` property. Also, I don't see any reference to this in the [GitHub wiki](https://github.com/OpenTreeOfLife/phylesystem-api/wiki/NexSON) or [WikiSpaces wiki](http://opentree.wikispaces.com/NexSON) about NexSON.

It's briefly mentioned in [this oti issue](https://github.com/OpenTreeOfLife/oti/issues/9) and it definitely sounds like legacy cruft.