Added sim init agents+prototypes tests and corresponding fixes.

* fixed manual modules map in DynamicModule to map to agent constructors -
  necessary to allow the newly constructed agents to be on the new context -
  Clone doesn't work.

* changed initial id's from 0 to 1

* set agent id in Agent::InitFrom(Backend) method.

* explicitly set agent id in sim_init LoadPrototypes

* delete sim_init's dummy agent's after using them so they don't pollute the
  context.