Urgh, getting constant struggles with Intel XDK now.
After being unable to build my app, I decided to fully reinstall Intel XDK, recreate the app from a blank file, and set it all up again. The build process then worked, or so I thought. Emulation was running perfectly. Everything finished uploading and building, I got my download link, installed the apk on my phone, but when I tried to run it, I got the error "Application Error (file:///android_asset/www/index.html)". I unpacked the apk and it turns out that there are no assets in the www folder!
Back in the XDK, I tried moving all the files to the root (instead of /www), but then the emulation can't find the files at all ("404: Intel XDK can't find your app".
Also, I'm getting the same emulation errors as Lof. This whole thing is a huge mess.
EDIT: Okay, it looks like I was a little overzealous with the axing of permissions. The building seems to be working fine now, but the emulation errors are still there. It also seems like all browser-related action (which generate errors in the emulation) aren't firing at all in the built app.