I executed emerge -DupvN world and got that: Calculating world dependencies... done! [ebuild U ] sys-apps/groff-1.19.2-r1 [1.19.1-r2] USE="X" 2,835 kB [ebuild R ] sys-apps/sysvinit-2.86-r5 USE="(-ibm) (-selinux) -static (-bootstrap%) (-build%)" 0 kB [ebuild R ] sys-libs/db-4.2.52_p2-r1 USE="java tcl%* -bootstrap -doc -nocxx -test% (-tcltk%*)" 0 kB [ebuild R ] perl-core/Test-Harness-2.56 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] perl-core/PodParser-1.32 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] sys-apps/file-4.17-r1 USE="python (-build%)" 0 kB [ebuild R ] dev-perl/XML-Parser-2.34 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Net-Daemon-0.38 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/PlRPC-0.2018 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/DBI-1.50 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/DBD-mysql-2.9007 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/TermReadKey-2.30 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] sys-apps/gawk-3.1.5-r2 USE="nls (-build%)" 0 kB [ebuild R ] net-analyzer/rrdtool-1.2.6-r1 USE="perl tcltk -doc (-minimal%)" 0 kB [ebuild R ] dev-perl/perl-tk-804.027 USE="(-minimal%) (-perl%*)" 0 kB [ebuild U ] dev-lang/php-4.4.4-r4 [4.4.3-r1] USE="apache2 bcmath berkdb bzip2 cdb cli concurrentmodphp crypt ctype curl dbase dbx doc exif expat flatfile ftp gd gdbm iconv imap iodbc ipv6 java-external ldap libedit mcal memlimit mhash ming mssql mysql ncurses nls odbc overload pcntl pcre posix session snmp sockets spell sqlite ssl sysvipc threads tokenizer truetype unicode xml xmlrpc xpm xsl zip zlib -adabas -apache -birdstep -calendar -cgi -cjk -db2 -dbmaker -debug -discard-path -empress -empress-bcs -esoob -fastbuild -fdftk -filepro -firebird -force-cgi-redirect -frontbase -gd-external -gmp -hardenedphp -hyperwave-api -informix -inifile -interbase -java-internal -kerberos -mcve -mnogosearch -msql -oci8 -oci8-instant-client -oracle7 -ovrimos -pfpro -pic -postgres -readline -recode -sapdb -sharedext -sharedmem -solid -sybase -sybase-ct -wddx -yaz" 4,393 kB [ebuild N ] dev-php4/php-java-bridge-2.0.8 0 kB [ebuild U ] media-libs/libsdl-1.2.11 [1.2.8-r1] USE="X aalib alsa esd fbcon libcaca nas opengl oss svga xv -arts -dga -directfb -ggi -noaudio -noflagstrip -nojoystick -novideo -xinerama (-pic%)" 2,730 kB [ebuild R ] dev-perl/XML-NamespaceSupport-1.09 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/XML-Simple-2.14 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] media-gfx/imagemagick-6.2.8.0 USE="X bzip2 jpeg jpeg2k lcms mpeg perl png tiff truetype wmf xml zlib -doc -fpx -graphviz -gs -jbig -nocxx (-minimal%)" 0 kB [ebuild R ] sys-apps/busybox-1.1.3 USE="-debug -make-symlinks -netboot -savedconfig -static (-floppyboot%)" 0 kB [ebuild R ] net-irc/irssi-0.8.10-r3 USE="ipv6 perl socks5 ssl (-minimal%)" 0 kB [ebuild R ] app-text/tetex-2.0.2-r8 USE="X tk%* -doc (-tcltk%*)" 0 kB [ebuild R ] dev-perl/Compress-Zlib-1.41 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/IO-Zlib-1.04 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/IO-String-1.08 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Archive-Tar-1.28 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Socket6-0.17 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/IO-Socket-INET6-2.51 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/DBD-SQLite-1.11 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/HTML-Tagset-3.10 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/HTML-Parser-3.48 USE="unicode (-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/URI-1.35 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/HTML-Tree-3.19.01 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/libwww-perl-5.803-r1 USE="ssl (-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Net-SSLeay-1.25 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/IO-Socket-SSL-0.97 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Convert-ASN1-0.19 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/perl-ldap-0.33 USE="ssl xml -sasl (-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Net-IP-1.24 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] perl-core/digest-base-1.13 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Digest-SHA1-2.11 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Digest-HMAC-1.01-r1 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] dev-perl/Net-DNS-0.53-r1 USE="ipv6 (-minimal%) (-perl%*)" 0 kB [ebuild R ] mail-filter/spamassassin-3.1.3 USE="berkdb ipv6 ldap mysql sqlite ssl -doc -postgres -qmail -tools (-minimal%) (-perl%*)" 0 kB [ebuild R ] sys-apps/net-tools-1.60-r11 USE="nls -static (-build%)" 220 kB [ebuild R ] net-print/foomatic-db-engine-3.0.2 USE="(-minimal%) (-perl%*)" 0 kB [ebuild R ] net-misc/ntp-4.2.2_p3 USE="caps ipv6 logrotate ssl -debug -parse-clocks (-selinux) (-openntpd%)" 0 kB [ebuild R ] dev-perl/Archive-Zip-1.16 USE="(-minimal%) (-perl%*)" 0 kB take a deeper look at perl modules: almost all have (-minimal%) (-perl%*), yet still I have perl flag set on as you can see in emerge --info attachment
Created attachment 96678 [details] emerge --info
This is not a bug, read the release notes. Those flags were removed (from the eclass), i.e. they changed.
