So there's probably something wrong with your main project. Does Run > Clean Project help at all?
Regarding Cppia, I wonder if it isn't being included since the compatibility of the extension is set to desktop. If you open info.txt within the extension folder and change "desktop" to "all", does the error with Cppia go away? I'd test it myself but I seem to have broken my Cppia setup when switching between 3.4 and 3.5.