Unify output directory

[nkrah]

All output data should be written into a unique (per simulation) output directory unless the user specifies an absolute path. This output directory is set via the user info Simulation.output_dir which will be prepended to the relative user-provided path/filename.

[nkrah]

The general feature, namely that a Simulation object has an attribute output_dir, is now available in the master. We have to go through the code and make sure that anywhere output data is written, the path is passed through the Simulation.get_output_path() function ...

[dsarrut]

#363