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You're developer #7,291 asking this question (and PGB isn't doing itself a service with the desktop app).
1. You should not upload a full Cordova project. Just upload your assets.
2. The config.xml should be in the root directory of your zip, along with index.html. The best way to do this:
- move config.xml into /www
- adjust the paths to icons/splashes
- zip up the contents of /www (not the directory itself).