Fix handling of unrecognised command line parameters

[Prof Garth Wells]

When parsing the global and PETSc parameters, legitimate user parameters lead to the annoying and misleading messge

"Skipping unrecognized option for parameter set . . ..

In parallel can be printed many thousands of times.

The message should not be printed, but a Parameters object could store unrecognised parameters for later inspection.

[Prof Garth Wells]

Fixed (more-or-less) in 95c6126.