Stop adding the dry-run option by default

Currently cli.py unconditionally adds the dry-run option. This patch
disables this, and exports dry-run as a normal option.

The other alternative I tried to implement (adding a new fake option for
disabling the auto-add per individual command) would require changes in
more places, as the list of options is no longer a homogeneous list.

Signed-off-by: Iustin Pop <iustin@google.com>
Reviewed-by: Michael Hanselmann <hansmi@google.com>