[gentoo-alt] Files in /$PREFIX/$PREFIX/

I see many files in /$PREFIX/$PREFIX/ that is /Library/Gentoo/Library/Gentoo on my PowerBook. I was re-emerging my system and I had a collision with a file in /Library/Gentoo/Library/Gentoo/usr/share/info/dir and I see that some packages are copying files in /$PREFIX and /$PREFIX/$PREFIX like here :
>>> Merging sys-devel/autoconf-2.13 to /
--- /Library/
--- /Library/Gentoo/
--- /Library/Gentoo/Library/
--- /Library/Gentoo/Library/Gentoo/
--- /Library/Gentoo/Library/Gentoo/usr/
--- /Library/Gentoo/Library/Gentoo/usr/bin/
>>> /Library/Gentoo/Library/Gentoo/usr/bin/autoconf-2.13
>>> /Library/Gentoo/Library/Gentoo/usr/bin/autoheader-2.13
>>> /Library/Gentoo/Library/Gentoo/usr/bin/autoreconf-2.13
>>> /Library/Gentoo/Library/Gentoo/usr/bin/autoscan- 2.13
>>> /Library/Gentoo/Library/Gentoo/usr/bin/autoupdate-2.13
>>> /Library/Gentoo/Library/Gentoo/usr/bin/ifnames-2.13
--- /Library/Gentoo/Library/Gentoo/usr/share/
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acconfig.h
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acfunctions
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acgeneral.m4
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acheaders
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acidentifiers
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acmakevars
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acoldnames.m4
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acprograms
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/acspecific.m4
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/autoconf.m4
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/autoconf.m4f
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/autoheader.m4
>>> /Library/Gentoo/Library/Gentoo/usr/share/autoconf/autoheader.m4f
--- /Library/Gentoo/Library/Gentoo/usr/share/info/
>>> /Library/Gentoo/Library/Gentoo/usr/share/info/autoconf.info
--- /Library/Gentoo/usr/
--- /Library/Gentoo/usr/share/
--- /Library/Gentoo/usr/share/doc/
--- /Library/Gentoo/usr/share/doc/autoconf-2.13/
>>> /Library/Gentoo/usr/share/doc/autoconf-2.13/AUTHORS.gz
>>> /Library/Gentoo/usr/share/doc/autoconf- 2.13/ChangeLog.0.gz
>>> /Library/Gentoo/usr/share/doc/autoconf-2.13/ChangeLog.1.gz
>>> /Library/Gentoo/usr/share/doc/autoconf-2.13/ChangeLog.gz
>>> /Library/Gentoo/usr/share/doc/autoconf- 2.13/NEWS.gz
>>> /Library/Gentoo/usr/share/doc/autoconf-2.13/README.gz
>>> /Library/Gentoo/usr/share/doc/autoconf-2.13/TODO.gz
>>> Safely unmerging already-installed instance...
<<<        obj /Library/Gentoo/usr/share/info/autoconf- 2.13.info.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/TODO.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/README.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/NEWS.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/ChangeLog.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/ChangeLog.1.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/ChangeLog.0.gz
--- !mtime obj /Library/Gentoo/usr/share/doc/autoconf-2.13/AUTHORS.gz

It must be an old problem and it may be solved but i did not found anything.
So, sorry if it is a stupid question.

Thanks.