Francois,

> I am running amavis chroot'ed.
> 
> I was thinking that SA reads its rules files before chroot takes place,
> so I keep using sa-update outside this chroot jail.

Unfortunately this is not the case.
 
> But despite running sa-update once a day, the Y2K10 bug was still hurting
> my configuration this morning...
> 
> Do I need to use --updatedir parameter in sa-update to put these files
> inside the chroot jail?

Correct.
Something like the following should be used (adjust the path as necessary):

# sa-update --updatedir /var/amavis/var/lib/spamassassin/3.003000

Also, make sure all the *.pre files are available in the jail:
/var/amavis/etc/mail/spamassassin/*.pre

I'll mention it in the README.chroot, thanks for pointing it out.

  Mark

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