Refactor off-by-default plugins and enabling them

We move the logic to add or remove a plugin from the default ignore
list to individual methods on the Plugin class (Plugin#enable,
Plugin#disable) and use that when registering and parsing options.

If the plugin is off-by-default, Plugin#register_options will use
Plugin#disable. When parsing options via Plugin#provide_options, if
the plugin has been specified in --enable-extensions then it will be
re-enabled via Plugin#enable.