So how do I tell sa-learn to use /var/mail/domain/user/.spamassassin/bayes_* instead of /root/.spamassassin/bayes_*
in local.cf or user_prefs add this config line:
bayes_path /var/mail/domain/user/.spamassassin/bayes
And yes, the bayes needs to be there even though it's part of the filename not the path.
See man Mail::SpamAssassin::Conf for more details.
Both spamassassin and sa-learn will honor this option.
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