plot: add a minimal elapsed time for step

The step signal was emitted each run of RootCoordinator::Run, the GUI thread
was overwhelmed. A minimal elapsed time of simulation of 100 ms is now required
before emitting the step signal.
plot: fix two issues

- time of simulation was based on the current state of coordinator.
- the mutex surrounding the RootCoordinator::run can make the Gui thread
  freezing if the run function is time consuming.