Merely emerging the kernel sources doesn't compile, install, nor reboot into a new kernel. Masking them should never be necessary. The most it will ever do is move the /usr/src/linux symlink to the new source tree for you, but only if you tell it to via the 'symlink' USE flag.
AFAIK, there are no packages which when emerged will restart automatically or do anything to existing processes. It's up to you to restart system services to load newer versions of the processes. (IOW no side effects.) /* PLUG: http://plug.org, #utah on irc.freenode.net Unsubscribe: http://plug.org/mailman/options/plug Don't fear the penguin. */
