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 on #920).

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.