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Allow overriding common cli options

Alexander Nørskov Larsen requested to merge 772-allow-overriding-cli-options into master

Adding new CLI options is breaking if we throw exceptions when overrides are detected. Let overrides replace the overriden option instead.

This only enables overriding for the --log and --help options. Allowing overrides for --color, --quiet and --verbose requires a bit more care because Environment.GetCommandLineArgs() is used sporadically throughout the code.

This merge request fixes the break, but we should probably clean up our usage of GetCommandLineArgs in a separate issue.

Closes #772 (closed)

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