Inconsistent configuration logic implementation

[curds01]

The configuration mechanism was intended with the following design:

1. Hard-coded default values serve as the default values.
2. Specifying the values in the project config file will replace the hard-coded values.
3. Any values provided on the command-line will trump all previous rules.

Currently, this isn't properly implemented. In mengeMain.cpp, the mapping from command-line arguments are handled incorrectly. The values for some unspecified command-line parameters are configured to render un-specified indistinguishable from configured.

• verbosity
• sub steps
• scb version
• seed

The solution is to change the command-line parser's default values and, in some cases, update the logic which conditionally sets the configuration parameters based on recognized user-values.

In some cases, it would be appropriate to issue a warning indicating recognition of a bad user-specified value.

[curds01]

In patching this, I noted that verbosity cannot be set in the configuration file; only on the command-line. So, its behavior can be left unchanged. Documentation is definitely lacking.

[curds01]

Closed by #77