You probably would need to use "Import Library ... -> Add Library ..." within Arduino IDE in order to make the compiler aware of your addition.
I guess following isn't recommended - still you might add it to hardware\tools\edison\sysroots\core2-32-poky-linux\usr\include where the compiler should find it out of the box
Have a look at the compile output in IDE console
Do you know if there is a verson of atomic.h that does work?
I see there are other copies of atomic.h. I'm not entirely sure how this directory structure works and which one corresponds to util/atomic.h.
For example, i see a copy here:
As well as here:
Is it possible that one of these may work? What path would I use to include these?