Add option to write each VR output to a separate directory

When running Velociraptor on the fly with many MPI ranks it generates a very large number of output files and makes an unreasonably large directory. This merge request adds a parameter which makes the code create a new directory for each output. If StructureFinding:subdir_per_output is specified then VR output files will have names like {subdir_per_output}_XXXX/stf\_{basename}_XXXX.*.

If we prepend to the output path like this then we can't include a directory in Snapshots:basename (this already didn't work in some cases because the code prepends 'stf_' to VR filenames). I've added a parameter Snapshots:subdir which can be used to put all snapshot and velociraptor output in the specified directory.

If neither parameter is specified then all files are written in the same locations as before.