Fix specifying a spec in the cli args

[SimonWoolf]

The custom spec wasn't getting the 'prefer-other' semantics of CFG#merge, so any spec specified by --specification in the args was getting ignored in favour of the default value of "Spec" from the base cfg.

Fixed by leaving it as None by default and merging as other.spec or self.spec, moving the "Spec" fallback to the last possible moment (format_cfg)