I am trying to update SpamAssassin's config on my server, since for whatever reason it thinks that DNSWL is whitelisting every incoming mail message. I put adjusted scores in /etc/mail/local.cf, but the settings are ignored. I think this is because update_spamassassin_org.cf is read afterwards and the individual included files in the update_spamassassin_org directory are read even later. These settings override my attempt to disable DNSWL and tweak some other items.
How can I get SpamAssassin to read local.cf (or some other file) at the VERY end of the config processing so that it overrides any other settings?
local.cf is always parsed second-last, immediately before the user-prefs. You need to have this file in the correct location for it to work (by default /etc/mail/spamassassin), but if it isn't doing what you expect, it's likely a problem with the directives you've specified (which you've not specified to us).