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Your options are either manually find what files are missing and I can send you a copy to paste back into your system or flash the stock image, this will mean you'll need to back up everything including your internal memory because it will wipe your whole N7...
With the ability to reinstall apps from Google Play, at this point why not just go with a factory reset? If rooted, you can then root again, install your apps, restore your data and you are done.