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What does rooted out mean?

There's two parts to rooting. First is the literal meaning of the word: obtaining root permissions to the filesystem. Apps can call su. The second is unlocking the bootloader and installing a custom recovery. With this in place, you can flash custom operating systems, create an image of your internal memory for backup (called a NANDroid backup), and squeeze out some more functionality from your hardware that maybe the manufacturer didn't fully utilize.
 
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Is Rooting your phone the same as the standard Android setup a Nexus phone has?
Apples and oranges. Rooting itself doesn't change the UI. See novox77's post again. Rooting specifically refers to what novox calls the "first part of rooting". The "other" part mentioned in the post technically isn't rooting though some people seem to lump it all together under the label "rooting". It's like how many apparently lump anything regarding determination of location as "GPS" whether the specific item discussed actually uses GPS or not.

does rooting expires your android warranty?
It voids it but it's not a permanent change. It's a software change that can be undone. If you need warranty support then revert before taking or sending the device in.
 
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