Write task dependency at every step

As the task are frequently modified during a simulation, we need a way to see the differences in the dependencies. Here I am adding a parameter Scheduler:dependency_graph_frequency. By default, we only write the 0-step and, if the parameter is set to 2, we dump every 2 steps.

I have also slightly modified the behavior of the task dependency graph. If I understand correctly, the scheduler is using only the dependencies of non skipped tasks. Therefore now I am only writing the non skipped tasks (except for the initial dump).

For the python script, we were still appending the data from different files together as initially we were dumping one file per rank. I removed this and replaced it by a loop over all the files in order to process multiple files at a time.