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68 configurable file output path

Afonso Mukai requested to merge 68_configurable_file_output_path into master

Created by: dominikwerder

A prefix for the HDF output filename given in the JSON write command can now be specified either on the command line via --hdf-output-prefix or in the JSON configuration file under key hdf-output-prefix. Added the parsing logic, unit tests and mentions the new option in README and the command line help. Closes #68 (closed).

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