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If you're cross compiling and want to add cpu specific flags globally, you may want to use eric's suggestion and include them in $ROS_ROOT/rosconfig.cmake. This is neater as it is under your control and avoids hacking someone else's CMakeLists.txt files (which will disappear next time you install).
If you need it for a certain package only, then that would be the only way to go, though I'd suggest finding a way to upstream the changes so others can benefit as well.