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So, your Qsys system is the only entity in your design and is your top level? What file(s) have you added to your Quartus project?
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Basically, yes. It's a design for Cyclone V so there is some additonal peripheral stuff for the hard processor system.
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You mention the "db" folders - you shouldn't be digging around in there. These are temporary files that Quartus uses/creates. They never contain design source that you need to add to your Quartus project.
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Ususally, I leave this folder alone. But the error orginiates from there: it contains the empty AHDL file. I certainly haven't added this file manually, but it is generated by Quartus.
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