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Change options from JSON to CLI

Afonso Mukai requested to merge DM-1818_CHange_options_from_json_to_CLI into v2_master

Created by: matthew-d-jones

Issue

DM-1818

Description of work

use_hdf_swmr and abort_on_uninitialised_stream were options that can be specified in the JSON command messages. Given that they will be used with default values per facility they are moved to options set on the command line or in the ini file. Documentation and system tests have been updated.

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