(chroot) localhost / # emerge -av --update --deep --newuse system

These are the packages that would be merged, in order:

Calculating system dependencies... done!
[ebuild     U ] sys-libs/pam-0.78-r5 [0.78-r3] USE="berkdb -nis -pam_chroot -pam_console -pam_timestamp -pwdb (-selinux)" 0 kB 

Total size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] y

>>> Emerging (1 of 1) sys-libs/pam-0.78-r5 to /
 * db-4.3.27.tar.gz MD5 ;-) ...                                           [ ok ]
 * db-4.3.27.tar.gz RMD160 ;-) ...                                        [ ok ]
 * db-4.3.27.tar.gz SHA1 ;-) ...                                          [ ok ]
 * db-4.3.27.tar.gz SHA256 ;-) ...                                        [ ok ]
 * db-4.3.27.tar.gz size ;-) ...                                          [ ok ]
 * Linux-PAM-0.78.tar.gz MD5 ;-) ...                                      [ ok ]
 * Linux-PAM-0.78.tar.gz RMD160 ;-) ...                                   [ ok ]
 * Linux-PAM-0.78.tar.gz SHA1 ;-) ...                                     [ ok ]
 * Linux-PAM-0.78.tar.gz SHA256 ;-) ...                                   [ ok ]
 * Linux-PAM-0.78.tar.gz size ;-) ...                                     [ ok ]
 * pam-0.78-patches-1.5.tar.bz2 MD5 ;-) ...                               [ ok ]
 * pam-0.78-patches-1.5.tar.bz2 RMD160 ;-) ...                            [ ok ]
 * pam-0.78-patches-1.5.tar.bz2 SHA1 ;-) ...                              [ ok ]
 * pam-0.78-patches-1.5.tar.bz2 SHA256 ;-) ...                            [ ok ]
 * pam-0.78-patches-1.5.tar.bz2 size ;-) ...                              [ ok ]
 * checking ebuild checksums ;-) ...                                      [ ok ]
 * checking auxfile checksums ;-) ...                                     [ ok ]
 * checking miscfile checksums ;-) ...                                    [ ok ]
 * checking Linux-PAM-0.78.tar.gz ;-) ...                                 [ ok ]
 * checking pam-0.78-patches-1.5.tar.bz2 ;-) ...                          [ ok ]
 * checking db-4.3.27.tar.gz ;-) ...                                      [ ok ]
!!! A file is not listed in the Manifest: '/usr/portage/sys-libs/pam/files/pam.d-0.99/other'