After reading about the la-files-checksum-mtime-unmerge-problem (at least) the second time and because I never liked the way lafilefixer worked, I decided to go the same way Diego does.
Because I use paludis I could not simply copy&paste the code, but writing a hook for paludis is really easy if you know what phase to hook into. I went with "merger_install_pre" and it seems to worked (I checked the CONTENTS file).
The code is an auto-hook, so just put it into "/etc/paludis/hooks/auto/lafilefixer.hook" and you should be fine. But I take no responsibility for killed kittens or other disasters ;-)
#!/usr/bin/env bash
hook_auto_names() {
echo "merger_install_pre"
}
hook_run_merger_install_pre() {
source ${PALUDIS_EBUILD_DIR}/echo_functions.bash
einfo_unhooked "Running lafilefixer"
lafilefixer ${IMAGE}
}