We do not want to duplicate items that are either in the student or teacher dashboards. With that said, which links are you concerned about?
I just added Calendar and Badges to the "This Course" drop down. So those links are taken care of already as of today.
I am thinking that Competencies will be added to the student and teacher dashboard popups.
I am still considering what to do with the custom menu items. I hit a snag. The My Courses and This Course menus piggyback off the custom menu renderer. This means my Fordson menus are generated at the same time that any custom links you might have made are created and they are all displayed at once. I need to split these items so that I can put custom links in their own area. I'll be working on this tomorrow.
If I can split the menus up then I can take care to put your custom links in a place that maximizes the screen real estate that they can occupy.
Currently in Moodle there are three areas a user must look for navigation and functionality: Nav Drawer (if they click the menu button), top navbar, and the gear when in a course. This is two places too many.
Tomorrow I plan on addressing the competencies link, splitting the custom menu from my Fordson Menus, and taking a stab at possibly putting blocks in where the nav drawer was previously while putting an icon that will open and close it in the middle of the screen. An icon with an arrow and maybe half circle in the middle-left of the screen. We are not crazy about putting the blocks in where the navdrawer was previously, but a lot of the coding work is already done.
We are determined to put the major navigation elements in one place and that looks like it will be the top nav bar across the entire top of the page.
Big picture: we are going to simplify navigation from within the Fordson theme and with this new approach it will train users to look in one place to make things happen. Even turn editing on will be in the top nav drawer and wherever you are in the course it will return you to that same spot once editing is turned on. We got that working at the end of the day.