The AndroidManifest.xml file will not exist since you are using PhoneGap Build.
Are properly zipping and uploading just the www folder to PhoneGap Build and within that directory is the config.xml file. I ask because the folders you list out look like you use one of the CLI to start your app.
The config.xml is in the root of the project folder ( where are all the folders listed above )
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That could be your issue. The config.xml file and the index.html need to be in the same directory and that be the at the root of the zip file you upload to PhoneGap Build. The Hooks, Platforms folder should not be included in to the zip file.
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