I tried to emerge courier 0.47. Got: >>> Completed installing into /var/tmp/portage/courier-0.47/image/ * checking 658 files for package collisions existing file /var/.keep is not owned by this package existing file /usr/.keep is not owned by this package existing file /var/run/.keep is not owned by this package existing file /usr/bin/.keep is not owned by this package existing file /usr/lib/.keep is not owned by this package existing file /usr/sbin/.keep is not owned by this package existing file /usr/share/man/.keep is not owned by this package * spend 0.527939081192 seconds checking for file collisions This does not look right. Reproducible: Always Steps to Reproduce: rescue / # emerge info Portage 2.0.51-r3 (default-x86-2004.2, gcc-3.4.2, glibc-2.3.4.20041102-r0, 2.4.27-040930 i686) ================================================================= System uname: 2.4.27-040930 i686 Intel(R) Celeron(R) CPU 2.00GHz Gentoo Base System version 1.6.5 distcc 2.18 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.3 [enabled] Autoconf: sys-devel/autoconf-2.59-r5 Automake: sys-devel/automake-1.8.5-r1 Binutils: sys-devel/binutils-2.15.92.0.2-r1 Headers: sys-kernel/linux26-headers-2.6.8.1-r1 Libtools: sys-devel/libtool-1.5.2-r6 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" COMPILER="" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs ccache collision-protect distlocks sandbox" GENTOO_MIRRORS="http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo http://194.117.158.29/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="acl apache2 apm arts async avi bzlib crypt cscope cups curl curlwrappers diet djbfft encode exif fam flash foomaticdb ftp fwdzone gd gdbm gif gnome gpm gtk gtk2 hal iconv imagemagick imap imlib immqt-bc javascript jpeg kde libedit libg++ libwww lzo lzw lzw-tiff mad maildir mailwrapper mbox mmap mmx mng mpeg ncurses nls no-old-linux noantlr nobcel nobeanutils nobsh nocommonslogging nocommonsnet nojdepend nojsch nojython nolog4j nooro noregexp norhino noxalan noxerces offensive oggvorbis opengl oss pam parse-clocks pcntl pcre pdflib perl pic pie png posix python qt quicktime readline recode sasl sdl shared slang sockets spell sse ssl sysvipc tcpd tiff truetype unicode x86 xfs xml2 xmms xv zlib linguas_de"
there is no actual data in the .keep files so its not like any critical data was going to get clobbered by it... but they weren't necessary either and have been taken out of the current ebuilds.