# As superuser
gentoo ~ # emerge --sync
gentoo ~ # emerge -av gentoolkit
gentoo ~ # emerge -av --newuse --deep --update world
gentoo ~ # emerge -av --depclean
gentoo ~ # revdep-rebuild
gentoo ~ # rm -rf /var/tmp/portage/*
gentoo ~ # rm -rf /var/tmp/ccache/*
gentoo ~ # rm -rf /var/tmp/binpkgs/*
gentoo ~ # rm -rf /var/tmp/genkernel/*
gentoo ~ # rm -rf /usr/portage/distfiles/*
gentoo ~ # rm -rf /tmp/*

First, you have to install gentoolkit if you haven done this already. Then we remerge or update all packages where USE flags have changed. Then we are searching for unneeded dependencies and remove them. Finally we check if there are any packages with unresolved link dependencies, let them emerge and then clean up some directories.

Optionally you can defrag some of your partitions if this is neccessary. In case of XFS you can do this by:

gentoo ~ # xfs_db -r /dev/hda2

After this you should have a cleaned up gentoo environment, with no broken dependencies and no unneeded packages or libraries.

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