Linux provides a method for allowing programs that need to compile against the kernel (such as kernel modules, nvidia-drivers for example) to know which version they should compile against. This is the /usr/src/linux symlink.
Gentoo additionally provides an easy tool for moving this symlink around, called kernel-config (It's actually part of eselect, so make sure that package is installed). To see a quick summary of how to use kernel-config, run it with no other options: kernel-config
Listing Available Sources
Now that the new kernel sources are installed, move the symlink to point to them using the following procedure. First list the available kernel sources with: kernel-config list
|Code: Example output of kernel-config|
Available kernel symlink targets:  linux-2.6.17-gentoo-r7  linux-126.96.36.199  linux-188.8.131.52-bb2  linux-184.108.40.206  linux-2.6.18-gentoo-r3  linux-2.6.18-gentoo-r4  linux-2.6.18-gentoo-r6 *  linux-2.6.18-usermode  linux-2.6.18-usermode_guest  linux-2.6.18-usermode-r1  linux-220.127.116.11  linux-18.104.22.168  linux-2.6.19-gentoo-r3  linux-2.6.19-gentoo-r3-guest  linux-2.6.19-gentoo-r3-skas-v9-pre9  linux-2.6.19-gentoo-r4  linux-2.6.20-rc5
the currently selected sources are marked with an ' * ' (for older versions run : readlink /usr/src/linux)
Changing the Target
Now set the symlink to the new kernel sources. For example, if the new sources are vanilla-sources 2.6.20-rc5, then run: kernel-config set 17
Alternatively, the sources directory name can also be used, for example: kernel-config set linux-2.6.20-rc5
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