Support for retroactively mature vaccine immunity

It appears that individuals who have never been infected before vaccination
are protected less effectively by the vaccine than those who already have
some immunity.  One possible scenario is that among individuals who are naive
at vaccination, subsequent infection boosts their immunity to other serotypes
as well.  This commit adds support for that option, currently called
-retroactivematurevaccine on the command line.

There's also a bit of refactoring and resolving some compile warnings.
Modified standalone EF estimator to use simple ABC