Hi maintainer,

This is a rather unfortunate bug.  As can be seen from the manpage,

  "Generally, the directives can occur in any order in the file and if a
  directive is specified multiple times, only the last one will be
  effective.  Exceptions are noted in the descriptions."

One of the potentially many configurations an end-user may need to adjust
is makestep, which is configured almost last in chrony.conf.

All VM's for instance, will need to customise that, so makes sense to
drop into /etc/chrony/conf.d/vm.conf:

  # ensure chrony doesn't bail if vmware gains or loses too many ticks
  makestep 1 -1

Well that's unfortunate, isn't it?  I now need to manually munge
/etc/chrony/chrony.conf of all of my generations of VMs.  And anything
else I've customised, I need to keep track of which of my machines are VMs
and which are not.

I just verified this *isn't* an upstream bug, with upstream not having
included a confdir directive at all.  It's also not fixed in 4.6.1-1 in
unstable.


It would be extremely nice to have this fixed for trixie.  It's
unfortunate that chrony is a regression over what we had with NTP, given
it is the claimed replacement of NTP and NTP fixed this issue 20 years
ago.



-- 
Tim Connors

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