Topic restart directories2

For issue #358 

- create checkpoints in additional directory within simOutput
- restart from that directory
- allow user to set directories application-wide (`--checkpoint-directory, --restart-directory`)
- allow to override application-wide settings with HDF5Writer settings

Both directories can be set as relative (to simOutput) or absolute. If `hdf5.restart-file` or `hdf5.checkpoint-file` is absolute, it overrides the application-wide directories.