Details
Bug
Major
Description
When a plugin is upgraded, all instances of the plugin on other companies are also upgraded since they share database tables. New permissions however are only added for the instance upgraded. This should be updated to add the permission for all plugin instances.
Activity
This new method will be similar to install() or upgrade() it will only receive plugin_id as the parameter and will return an array of all the plugin permissions, the plugin manager should be updated as well, as will need to add the permissions during installation and check what new permissions should be added on upgrade as well for all companies.
I see. Well in that case I don't think there is any need to make this backward incompatible. It is simple enough to create a default method on the Plugin class that returns an empty array. Then all plugins that don't implement the method will continue to function in the current fashion.
Is there a need for the $plugin_id parameter? It is just getting a list of permissions, yes?
We'll also probably want to remove the permissions on uninstall. Upgrade should check permissions on every instance of the plugin, while install and uninstall should only effect the particular plugin the action is being taken on.
Do we have what we need to get started on this? I'd love to get 4.9.1 out by the end of the week.
I think we can remove the $plugin_id parameter as the method will only return a list of permissions, I see it possible to have it ready by the end of the week. 
I've got some time this afternoon so I'll go ahead and pick this one up and let you focus on filtering
The only backward compatible integration I see here is to assume the plugin will set permissions for all copies of the plugin during upgrade. So the solution would be for each plugin to implement any permissions across all installed plugins. The plugin system would have to be refactored to change the way that plugins handle multiple instances of a single copy and that would require a major version change to accomplish, and likely updates to all plugins.