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How to file messages to folders only after you finished processing it in your Inbox

What you can do is add an Outlook Category to the message when you are done with it and want it to be filed. Then set the Auto-Mate rules to only move messages marked with that Category.
Start be setting the rule to scan messages in your source folder after a period of time. It can be set to scan as frequently as once every 15 minutes, or once per hour (choose any time value > 15 minutes)
Then on the Message properties tab, set the rule to only files marked with category "To File". You can name the Category anything you like of course.
Then set your actions to file your message. You can even clear the Category:
Then all you have to do to have Auto-Mate file the messages for you is to tag the messages you want filed with the To category.