Remove site specific global flags

`php/config-spec.php` defines flags that can be passed to **any** command i.e. `--debug`.

However it contains following flags which are site specific which needs to be removed - `sites_path`,`locale`(for wordpress), `le-mail`.

One advantage of adding these flags is that it automatically searches from config file for these variables and gets their values. However, since we've moved every site specific thing from core to their packages, it makes no sense to keep package specific flags here.

Also wherever these flags are used in other commands, we need to add local flags(to command) and also ensure that these values are read from config file so that earlier behaviour is preserved.