I notice that my eix DBs have been gradually becoming out-of-sync with
my ebuild repos. eix-update shows no errors but always says there are
the same number of packages.

Strace shows about 10k open errors:

 ~ # strace -fcw eix-update >/dev/null
% time     seconds  usecs/call     calls    errors syscall
------ ----------- ----------- --------- --------- ----------------
 34.11    0.492491           6     87192           read
 28.34    0.409197           6     63923     10066 open
 20.40    0.294469           5     53857           close
  6.03    0.087096           9      9972           getdents
  3.84    0.055440           5     10570           fstat
[...]

However most of these are only metadata/md5-cache files under my layman
directory, not the main portage tree. I have no idea what those files
are for anyway since there's no documentation.

It does seem to be doing something with the eix db itself as mtime is
changed - just no changes are reflected when querying it, even the
main repo. e.g.:

 ~ # eix -e portage
[?] sys-apps/portage
     Available versions:  2.2.26 2.2.28 2.3.0{tbz2} (~)2.3.1 (~)2.3.2 2.3.3 
**9999 {build doc epydoc +ipc (+)native-extensions selinux xattr LINGUAS="ru" 
PYTHON_TARGETS="pypy python2_7 python3_4 python3_5 python3_6"}
     Installed versions:  2.3.5(02:47:21 AM 03/18/2017)(doc ipc 
native-extensions xattr -build -epydoc -selinux LINGUAS="-ru" 
PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6 -pypy")
     Homepage:            https://wiki.gentoo.org/wiki/Project:Portage
     Description:         Portage is the package management and distribution 
system for Gentoo

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