Run inter-period optimizers even for first stage

This makes a bit more sense: stage 0 is a setup stage in which nothing
happens, but a transition between initial state and t=1 state shouldn't
be any different than any other transition.  If, for example, you
capture the state in t=37, then restore that state in a new simulation
at t=0, presumably t=1 of the new simulation should (at least
probabilistically) end up where t=38 of the old simulation would have
ended up.

Since this is a fairly major behaviour change, I'm also incrementing the
eris version to 0.2.0.
Improved docs; added seed(s); avoid unique_ptr

Adding seed(s) exposed a clang bug when referencing a thread_local
std::unique_ptr (reported as debian bug #755211): work around it by
not bothering with the unique_ptr at all (reseeding the initial object
before it gets returned from the first rng() call).