The Canvas elementary theme adjusts the course navigation.  When looking at the course menu in the settings page (called "Manage Subject" in elementary theme), some Cidi Labs LTI tools such as TidyUP or Multi-Tool may be enabled in the navigation settings but appear missing from the course menu list.  However, you should still be able to access these tools from the Home screen.

While in the home screen of the course, click the Resources option and you should be able to see all the Cidi Labs LTI tools.