Internal memory not being erased?

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I wanted to wipe my phone back to stock, so I did a Factory data reset in the Setting>Power menu. After it completed I connected the phone in disk drive mode, but it still had many of my old app folders in the root.

How can I get rid of these folders and go back to how I got my phone from ATT?

you can flash the RUU thats in the dev forums, it should wipe the phone.

i haven't tried to wipe this phone yet, but on my gnex, iirc, there was an option when you asked it to wipe to remove all personal data as well. i'll have to check for it on my 1x after i finish flashing the new RUU to it.

edit:

i looked again, it's in settings / storage. in there it has options to wipe saved data from the apps partition as well as the sdcard partition, and also the factory wipe.