ah ok.
You can do it as you prefer.
I do not think there are rules / suggestions about the project structure.
And in the report you could simply list your files / folders.
I do not know if there is an "elegant" organization. You could place a DApp/ folder inside your Truffle project folder, together with contracts/, tests/ etc etc. For the purposes of the project I think is enough. For bigger projects then I think it is like to structure a complete web application