fix/nekmesh-config-default

This fixes a subtle bug with the config options in nekmesh.

For example, running the command -m jac:extract. Which has a default numerical value of 0 associated with it would actually have a value of 1. This was partly because the isBool and beenSet parameters were not being dealt with quite correctly. Now when specifying a config option which is not bool and has a default value without the user giving a value will correctly use the hard coded default.