Check that file output directories exist

[cpethrick]

Add logic to the parameters parsing sections to ensure that output directories exist. I chose to abort rather than create the missing directories to prevent cases where someone may have launched from the wrong working directory or otherwise made a mistake in their simulation setup. I could be persuaded to just create missing directories, though.

The change is motivated by the following deal.ii error message, which gives a correct but overly general diagnosis of the problem.

[sonarcloud[bot]]

Kudos, SonarCloud Quality Gate passed!   

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