I have a script (found here on github) that custom compiles the 3.8 linux kernel (with Xenomai for real-time). The kernel compiles/installs/runs however when I try to install my graphics driver (fglrx for ATI RADEON 8490), I get the following error:

/lib/modules/3.8.13.20-xenomai-2.6.3/build/include/generated/uapi/linux/version.h cannot be found on this system.

When I look into this directory (/lib/modules/3.8.13.20-xenomai-2.6.3/build/) there is nothing there. I then ran an ls -l in /lib/modules/3.8.13.20-xenomai-2.6.3 and got the following output for the build directory:

build -> /home/yapatel/Dev/rtxi/scripts/linux-3.8.13

The directory that the build directory is pointing to was deleted as a part of the script for compiling/installing the custom kernel so this symbolic link is dead, which make sense as to why I am getting the error.

I am compiling the custom kernel using the following command:

fakeroot make-kpkg --initrd --append-to-version=-xenomai-$xenomai_version kernel-image kernel-headers modules

and then installing the compiled kernel using the following commands:

sudo dpkg -i linux-image-*.deb

sudo dpkg -i linux-headers*.deb

sudo update-initramfs -c -k $linux_version-xenomai-$xenomai_version

sudo update-grub

Now here is my question - I understood it as the above installation commands to take care of all the necessary pieces for installing a custom compiled kernel, however the deadlink to my build directory seems to suggest that I need to manually copy over the files from:

/home/yapatel/Dev/rtxi/scripts/linux-3.8.13

to

/lib/modules/3.8.13.20-xenomai-2.6.3/build/

This seems like a manuall fix rather than the proper fix. Is there a command I am missing in the compile/install process of my custom kernel? I am assuming this means my kernel modules are not being installed?

All advice/help is appreciated!