#9 MOOSE Model Builder only writing out "required" parameters

[Anna Wojtowicz]

The MOOSE Model Builder is only writing out parameters whose entries have the required = true flag set, and skipping over everything else, including custom parameters.

This is why BISON didn't error out when launching a problem with both a mesh file and a type specified -- none of the SmearedPelletMesh stuff was actually written out, and so it executed using the mesh file as usual.

[Anna Wojtowicz]

Changed the MOOSE file writer, so in addition to all parameters marked as required, it will also write out non-required parameters with valid/non-empty values.

In the meantime, this does mean that the input files will have a lot of extra default parameters from the YAML spec written out, which is just redundant, but this will be remedied soon enough when we enable parameter deletion and/or commenting out.