Output and trajectory files don't match about smac3

[mlindauer]

(similar to checking the configuration budgets)
the trajectory file is only updated after each iteration.
Since we run at least two (in this example probably even more) configurations in each iterations,
it can happen that we change the incumbent more than once per iteration and the trajectory is updated only once.

We could pass the TrajLogger object also to Intensifier, but I would like to avoid this because the class has already quite a lot to handle.

However, I found another bug related this issue.
We first checked whether the configuration budget was empty and updated the trajectory file afterwards if the configuration was not empty. Therefore, we would not save the last incumbent in the trajectory file.

[mfeurer]

@KEggensperger can this be closed?