Save values (cli options) passed manually and merge with defaults

We need to save manually passed values in order to prevent using default values in `PHP_CodeSniffer::process` (`$cliValues = $this->cli->getCommandLineValues()`)

I'm not sure if this is acceptable, so I made simple changes in previous PR (https://github.com/squizlabs/PHP_CodeSniffer/pull/172). Choose which one better reflects your vision of doing this.