Similar issue, after I used $xenomai_root/configure --enable-x86-sep for a i386, and make install.  I can't do any make, such as make clean, make menuconfig.
The message was: make: *** No rule to make target 'clean'. Stop.
I had to remove the build and start over.
This issue happened regardless to different combination of kernel and xenomai.
The question is: Do I need to enable-x86-sep for i386.  If yes, how can I get vmlinux, initrd, System.map under /boot? Any suggestion to resolve the build problem?
Thanks,
Dennis

PS: I used make install after the $xenomai/configure --enable-x86-sep.

Dennis Nguyen <dennisnguy@domain.hid> wrote:
I followed the README from xenomai to build kernel+xenomai:
-prepare-kernel.sh ...
cd $linux_tree
make menuconfig
make bzImage modules
make modules_install

When ever I used $xenomai_root/configure --enable-x86-sep, It won't
create System.map vmlinux, and initrd under/boot.

I used different combo kernel linux-2.6.20.10 with xenomai-2.3.4.
kernel linux-2.6.22.10 with xenomai-2.4-rc4.
kernel linux-2.6.22.10 with xenomai 2.4-rc5.
The result for the System.map vmlinux, and initrd under /boot are the
same. If I do not used the configure --enable-x86-sep then the files
built under /boot.

Any suggestion please,
Thanks
Dennis