Update for boolean option flags passed to CLI. Fixes #920

When boolean options are passed along with secondary flags, those secondary flags become the value for the boolean (shown in the issue report).

This is caused by how the arguments are passed to `nopt` to pull those pieces together.  This update simply iterates against the arguments in the process list (`process.argv`) and for those that are a flag without a value (e.g. `--build`) it will assign append an `=true` to the value.

Not sure this is the most elegant fix, but it is simple and does cause flags to be parsed appropriately.