Allow discover mode to use -u, -c, -D, etc options

After discussing with a fellow engineer here at Urban Mapping, we decided it makes sense to support the use case where a user would want to use these flags with the "discover" mode.  For example, they may want to point their collection of benchmarks at a different staging server with -u.  Or they may want to debug all their XML result files, so they want to use -D 1.