Andy Lee at Arrow recommended copying the .vhd and .v files from the "synthesis" and "submodules" folders to the main project folder. Doing so remedies the 12006 error shown above. Andy's email is below.
From: Andy Lee
You can add those files in assignments->settings->files and some people do it that way, but I prefer to copy them into the project directory. Anything in the project directory will get automatically picked up.
But, it is a personal preference, if you were to make changes to that IP, and regenerate it, you would have to copy the files over again. I think Altera recommends doing it that way because you could ostensibly create different versions of that IP and keep them around as you try different things out, maybe not for a uart, but for something that might need different revisions to achieve different things.
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