fix(plugins): trigger plugin hooks when saving plugin settings

$plugin->setPrivateSetting doesn't trigger plugin hooks. 

Calling $plugin->set instead trigger plugin hooks and internally calls $plugin->setPrivateSetting

Fixes: #6820

TODO:

* [x] Document why ```setSetting()``` is replace with a key = value pair
* [ ] Update commit message to match Elgg standards, remove semicolon after Fixes