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According to the home page for the script
http://www.exit0.us/index.php?pagename=RulesDuJour
Add a TRUSTED_RULESETS line to your config file that contains the
names of the rulesets you chose. Example below:
* TRUSTED_RULESETS="TRIPWIRE SARE_ADULT SARE_OBFU0 SARE_OBFU1
SARE_URI0 SARE_URI1"
Well, you copy your rulesdujour script configuration section to
/etc/rulesdujour or some other place were you have config files - there
are a list of places/file where it looks for a config file in the first
few lines of the script.
that is where you set the paths for spamassassin and rules you want to
check and other options that over ride the defaults that are in the script.
then you can upgrade rulesdujour whenever there is an update and you
don't loose your list of rules by overwriting the script.