Compendium Permissions is a simple module that enables GM's to set view permissions on compendiums individually between their players.
Simply right click on a compendium and choose Configure Permissions, and a prompt rather similar to the core Foundry permission configuration window will open.
You can mass change permission for all players by using the first option, or you can change them individually. Changes are performed real time, and all connected clients will automatically have their compendium sidebar refreshed as you adjust permissions.