If you build locally, using PhoneGap CLI or Cordova CLI, you can do whatever you want. PGB only accepts your "www" folder, so you aren't going to be pushing your own native code up as well. If what you need is available via a plugin, PGB may be able to use it (there are some exceptions: no hooks, for example). If you're a paying customer, you can upload your own private plugins. I think as far as extensions go for widgets and such, though, you have to make changes to the Xcode project at the moment in order to get that to work, something you'll only be able do locally.
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