Decouple `Manager` simulations from `AnalysisSet::step()` and `Storage` accumulation

[nickbianco]

Manager currently records simulation results by calling AnalysisSet::step and accumulating states in a Storage on the fly. If a Storage is populated, then it also calls ControllerSet::storeControls at each time step. This coupling invites future bugs if changes are made to analyses or Storage that don't consider how Manager operates.

Ideally, a trajectory of states is stored during a simulation and then an analysis or conversion to Storage can be perform post-hoc.