Conflict with plugin which filter `active_plugins`

[willmot]

We have a conflict with the Plugin Organiser plugin because of the way we reorganize the active_plugins array in https://github.com/humanmade/backupwordpress/blob/master/classes/class-plugin.php#L325:L346

Plugin Organizer allows users to hide plugins from the Plugins list table, it does this by filtering the array of active_plugins and removing plugins that are hidden.

Because we pull the list of active plugins and then save back to the database we’re having the side effect of saving back the modified list after Plugin Organizer has removed the hidden ones, this then causes them to become deactivated.

See https://wordpress.org/support/topic/it-disables-plugin-and-leave-it-that-way/ for more detail.

Question, do we actually need to save back to the database, can’t we just rely on rejigging the order at run-time?