Merge branch 'cmd-line-parameters' into 'master'

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

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.

See merge request !353