Is it possible to disable notification generated by Mail.app for a certain set of folders?
For e.g. if have
Inbox > fol1 &
Inbox > fol2, I want notification from
Would this be possible with growl somehow?
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You should be able to do this by setting up Rules in Mail.app that filter on the criteria you desire and then run an AppleScript that triggers a Growl notification. Rules are setup in Mail.app under Preferences…->Rules.
Growl can be called from AppleScript as shown here.
Use Smart Mailboxes to filter the mailboxes viewable,