If you are updating your Xen installation from 3.x to 4.x you may encounter something like this:

>>> Installing (1 of 3) app-emulation/xen-tools-4.1.0-r1
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / ` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). Once again, please do NOT file
 * a bug report unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 *      /usr/include/xen/COPYING
 *      /usr/include/xen/arch-ia64.h
 *      /usr/include/xen/arch-x86_32.h
 *      /usr/include/xen/arch-x86_64.h
 *      /usr/include/xen/callback.h
 *      /usr/include/xen/dom0_ops.h
 *      /usr/include/xen/domctl.h
 *      /usr/include/xen/elfnote.h
 *      /usr/include/xen/event_channel.h
 *      /usr/include/xen/features.h
 *      /usr/include/xen/grant_table.h
 *      /usr/include/xen/kexec.h
 *      /usr/include/xen/memory.h
 *      /usr/include/xen/nmi.h
 *      /usr/include/xen/physdev.h
 *      /usr/include/xen/platform.h
 *      /usr/include/xen/sched.h
 *      /usr/include/xen/sysctl.h
 *      /usr/include/xen/trace.h
 *      /usr/include/xen/vcpu.h
 *      /usr/include/xen/version.h
 *      /usr/include/xen/xen-compat.h
 *      /usr/include/xen/xen.h
 *      /usr/include/xen/xencomm.h
 *      /usr/include/xen/xenoprof.h
 *      /usr/include/xen/arch-x86/xen-x86_32.h
 *      /usr/include/xen/arch-x86/xen-x86_64.h
 *      /usr/include/xen/arch-x86/xen.h
 *      /usr/include/xen/foreign/ia64.h
 *      /usr/include/xen/foreign/x86_32.h
 *      /usr/include/xen/foreign/x86_64.h
 *      /usr/include/xen/hvm/e820.h
 *      /usr/include/xen/hvm/hvm_info_table.h
 *      /usr/include/xen/hvm/hvm_op.h
 *      /usr/include/xen/hvm/ioreq.h
 *      /usr/include/xen/hvm/params.h
 *      /usr/include/xen/hvm/save.h
 *      /usr/include/xen/io/blkif.h
 *      /usr/include/xen/io/console.h
 *      /usr/include/xen/io/fbif.h
 *      /usr/include/xen/io/kbdif.h
 *      /usr/include/xen/io/netif.h
 *      /usr/include/xen/io/pciif.h
 *      /usr/include/xen/io/protocols.h
 *      /usr/include/xen/io/ring.h
 *      /usr/include/xen/io/tpmif.h
 *      /usr/include/xen/io/xenbus.h
 *      /usr/include/xen/io/xs_wire.h
 *      /usr/include/xen/xsm/acm.h
 *      /usr/include/xen/xsm/acm_ops.h
 *      /usr/include/xen/xsm/flask_op.h
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * app-emulation/xen-3.2.1
 *      /usr/include/xen/COPYING
 *      /usr/include/xen/arch-ia64.h
 *      /usr/include/xen/arch-x86_32.h
 *      /usr/include/xen/arch-x86_64.h
 *      /usr/include/xen/callback.h
 *      /usr/include/xen/dom0_ops.h
 *      /usr/include/xen/domctl.h
 *      /usr/include/xen/elfnote.h
 *      /usr/include/xen/event_channel.h
 *      /usr/include/xen/features.h
 *      /usr/include/xen/grant_table.h
 *      /usr/include/xen/kexec.h
 *      /usr/include/xen/memory.h
 *      /usr/include/xen/nmi.h
 *      /usr/include/xen/physdev.h
 *      /usr/include/xen/platform.h
 *      /usr/include/xen/sched.h
 *      /usr/include/xen/sysctl.h
 *      /usr/include/xen/trace.h
 *      /usr/include/xen/vcpu.h
 * 
 * Package 'app-emulation/xen-tools-4.1.0-r1' NOT merged due to file
 * collisions. If necessary, refer to your elog messages for the whole
 * content of the above message.

>>> Failed to install app-emulation/xen-tools-4.1.0-r1

This problem arises because the new version of xen-tools takes over installing some of the files the old version of xen used to:

# portageq owners / /usr/include/xen/COPYING
app-emulation/xen-3.2.1
        /usr/include/xen/COPYING

To fix, unmerge the old version of xen then emerge --update xen to install the new versions of the xen-tools and xen packages:

# emerge --unmerge xen
# emerge --update --deep --newuse xen