When a web application is unmerged, the files for the installed versions change permissions. Permissions for installed versions are expected not to change. Installed version of webapp-config is 1.50.16-r1. Steps to reproduce: With the vhosts flag on: 1. emerge =phpmyadmin-2.11.5.2 2. webapp-config -I -d mysql phpmyadmin 2.11.5.2 3. cd /var/www/localhost/htdocs/mysql 4. ls -l (permissions correct - files are 644, root:root) 5. emerge -C =phpmyadmin-2.11.5.2 6. ls -l (permissions INCORRECT - files are 000, root:root) Portage 2.1.4.4 (default/linux/x86/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.21-xen x86_64) ================================================================= System uname: 2.6.21-xen x86_64 AMD Athlon(tm) 64 Processor 3000+ Timestamp of tree: Fri, 18 Jul 2008 13:33:01 +0000 app-shells/bash: 3.2_p33 dev-lang/python: 2.5.2-r5 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.61-r2 sys-devel/automake: 1.7.9-r1, 1.10.1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -pipe -mno-tls-direct-seg-refs" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/init.d /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d /usr/share/X11/xkb" CXXFLAGS="-O2 -march=i686 -pipe -mno-tls-direct-seg-refs" DISTDIR="/mnt/portage/distfiles" EMERGE_DEFAULT_OPTS="-vat --with-bdeps=y --alphabetical" FEATURES="buildpkg collision-protect distlocks fixpackages metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS=" http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo http://mirror.switch.ch/mirror/gentoo/ http://pandemonium.tiscali.de/pub/gentoo/ " LDFLAGS="-Wl,-O1" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/mnt/portage/local/rsync_excludes" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/mnt/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="acl apache2 bash-completion bzip2 cli cracklib crypt cups dri fortran iconv ipv6 isdnlog ithreads midi mudflap ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline reflection session spl ssl tcpd threads unicode vhosts x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="fbdev glint i810 mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTDIR_OVERLAY
Looks like a security feature to me, but let's hand it over to the experts. :)
I am not able to reproduce this with webapp-config 1.51. I'm not sure what changed, but the entire /var/www/localhost/htdocs/mysql is removed making the bug obsolete.
