Those folders are part of how Nginx operates (buffering requests/responses are written to disk). You can configure the locations of those folders (or turn them off) with various nginx configs or at build time via the configure script. But disabling proxy buffering is generally not recommended unless you know what you're doing. I suppose you could also disable whatever unnecessary proxying protocols you don't need via compile-time options as well.
As far as your project layout, I suggest you either configure them to live elsewhere or learn to live with them. :)
