I'm trying to add local rules, but only one of the .cf files in /etc/mail/spamassassin seems to be used. Can you only have one extra .cf file? (I'm using amavis with SA, so I was told the extra rules can't go in local.cf).
SA should use _every_ file that matches /etc/mail/spamassassin/*.cf
HOWEVER, it is extremely important that you run spamassassin --lint whenever you change a configfile.
A syntax error can cause SA to ignore the entire file, and may even cause it to ignore rules in _other_ files too. Most notably, forgetting a trailing / on a regex will very severely confuse the rule processor.
I suspect your local rules might be getting ignored due to a syntax error. This is the cause of the vast majority of "ignoring new settings".
Also, if you use spamd, you must restart spamd every time you change /etc/mail/spamassassin/*.cf... to save overhead spamd only parses these files when it starts, instead of every time a message arrives.
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