What I usually do in that kind of situation is to mask the package
I don't want, and retry. Then emerge tell me what is depending on it,
and I check if some use flags can solve the problem, or I also mask this
second package, etc., until I find what I can unmerge or which use flag
to change to solve the issue.

 % mkdir -p /etc/portage    (in case you don't have one already)
 % echo "x11-base/xfree" >> /etc/portage/package.mask
 % emerge -Duvp world

You should get this error message:

!!! all ebuilds that could satisfy "virtual/x11" have been masked.
!!!    (dependency required by "xxxxx/yyyy-1.2.3" [ebuild])

It will be a good starting point to track the issue up to its origin.


-- 
TGL.

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