Change options from JSON to CLI
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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