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One thing you can do to make dependency tracker less annoying and tedious is to open up your database (for me it is SSMS) and then right click on the specific object or objects and "View Dependency Diagram". From here you can resolve missing dependencies on an object-by-object basis. It would be nice if selecting specific objects in Dependency Tracker actually worked but for now what i stated above is fairly painless. / comments
One thing you can do to make dependency tracker less annoying and tedious is to open up your database (for me it is SSMS) and then right click on the specific object or objects and "View Dependency...