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Add -P command-line option to overwrite or add program parameters

Merged Peter W. Draper requested to merge cmd-line-parameters into master

So you can run commands like:

 ../swift -s -t 4 -PTimeIntegration:time_end:1 -PDomainDecomposition:repartition_type:edge_weights sodShock.yml

and avoid editing the YML file. These parameters will overwrite any values already read from the YML file or added new parameters as necessary.

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