Using "eselect repository remove" leaves an empty line at the end when removing the latest entry from /etc/portage/repos.conf repos.conf before adding additional repository: $ cat /etc/portage/repos.conf [testing] location = /var/db/repos/testing auto-sync = no [brother-overlay] location = /var/db/repos/brother-overlay sync-type = git sync-uri = https://github.com/gentoo-mirror/brother-overlay.git [gentoo] location = /var/db/repos/gentoo sync-type = rsync sync-uri = rsync://rsync.de.gentoo.org/gentoo-portage/ After "eselect repository enable vortex" $ cat /etc/portage/repos.conf [testing] location = /var/db/repos/testing auto-sync = no [brother-overlay] location = /var/db/repos/brother-overlay sync-type = git sync-uri = https://github.com/gentoo-mirror/brother-overlay.git [gentoo] location = /var/db/repos/gentoo sync-type = rsync sync-uri = rsync://rsync.de.gentoo.org/gentoo-portage/ [vortex] location = /var/db/repos/vortex sync-type = git sync-uri = https://github.com/gentoo-mirror/vortex.git After "eselect repository remove vortex" there is an empty line at the end. After again "eselect repository enable vortex" $ cat /etc/portage/repos.conf [testing] location = /var/db/repos/testing auto-sync = no [brother-overlay] location = /var/db/repos/brother-overlay sync-type = git sync-uri = https://github.com/gentoo-mirror/brother-overlay.git [gentoo] location = /var/db/repos/gentoo sync-type = rsync sync-uri = rsync://rsync.de.gentoo.org/gentoo-portage/ [vortex] location = /var/db/repos/vortex sync-type = git sync-uri = https://github.com/gentoo-mirror/vortex.git So empty lines are getting more and more between the entries.