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Every incoming e-mail is filtered by some e-mail filter rules, based on a language called Sieve.

E-mail filters rules include: vacation, forward, spam filters, general filter rules. These 4 points (your main filter settings included) can be managed using webmail service ONLY (at the moment the interface of Horde is the only webmail service available). The old one, based on Procmail, is now disabled.
All e-mail clients (pine, thunderbird, etc.) filter rules work after the rules managed through webmail service (horde), so any e-mail client can not overwrite or overtake the rules fixed/managed through webmail service.

If you define a rule through webmail service, this will be active until when you change or overwrite it. The activated filters are the ones which have been saved for last.