I think I have everything working except that it doesn't seem to take the user_prefs in
/home/user/.spamassassin into account. Is there extra configuration neccessary for SA to
use the user's user prefs into consideration?
No, although by default "rules" are ignored in user_prefs when using spamd for security. "rules" means body, rawbody, header, uri, and anyother statement that creates a regex. I'm not sure if meta statements are ignored or not, but I'd assume so.
Other config options are still honored, including score statements.
One thing you might need to check however is that SA by default only honors the user_prefs file for the user that EXECUTES it (ie: not the one addressed in the email, but the userid of the process when it's executed.)
You can pass a -u parameter to spamc to cause spamd to setuid to another user prior to processing, thus getting another user's home dir.
You might also want to try checking for configfile syntax errors with spamassassin --lint
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