Unless anything has recently changed as far as i'm aware you can't really do much with the files on your PC at this point. I've mainly used this to save a few betas I was apart of.
User content such as saves is synced to the cloud.
If you managed to extract the installed games from one external hard drive i'd imagine you will be able to copy them back. It might be safer to just copy them to an external usb drive then you can copy them back to the internal hard drive if desired on the Xbox One its self. That way you don't have to open your new Xbox One and void the warranty.
Does this work with a flash drive formatted for Xbox one?My theory is that will happen if you fill the internal hard drive, however i'm no where near doing that to test it.