Ubuntu – Wrong kernel version returned by uname Ubuntu 16.04.1 LT

I don't have specific experience with ClearLinux, but it looks like you can:

# It's best to first compile their gcc (https://github.com/clearlinux-pkgs/gcc)
mkdir ~/patched_source
git clone https://github.com/clearlinux-pkgs/linux ~/clearlinux_patches
cd ~/clearlinux_patches
./scripts/develop.sh linux.spec ~/patched_source

That should download the upstream kernel to a folder below ~/patched_source (it will tell you the exact name) and apply ClearLinux's own patches and default config.

You can then proceed to compile the kernel as usual, for instance:

cd that_folder
CC=/the/clearlinux/gcc make -j4 bindeb-pkg
# This will take a while and create a few linux-xxx.deb files in the parent directory
sudo dpkg -i ../*.deb   # Or just the latest

Disabling the CONFIG_RETPOLINE mitigation makes it possible to compile with Ubuntu's gcc (at a cost, obviously).

The usual warnings apply: try in a VM first, secure boot can be tricky, there might be some Ubuntu-specific patches missing, ...

If you feel adventurous you can also add some of their own cmdline options to /etc/default/grub (like the ones in lines 8-15)