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I have Thunderbird set up to use my Gmail account through IMAP. All works well and good, except for one problem:

I have a group of gmail mail filters set up to redirect mail into different labels based on what it's for. However, by default, it seems Thunderbird only checks the Inbox for new messages. Is there a way to get it to check the subfolders aswell?

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I do exactly the same.

If you right click on a folder, then select properties, there is a check box that says "Check this folder for new messages". That's the one you want!

Unfortunately I don't think there is any way to do this for all folders at once, you have to do them one by one.

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It can be done, similar to Thunderbird 2: Tools - Options - Advanced - Config Editor, then set "mail.check_all_imap_folders_for_new" to "true".

In Thunderbird 8 the property is called "mail.server.default.check_all_folders_for_new"

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Thunderbird 3 will automatically update/refresh individual IMAP folders when you switch to them (e.g. click on them). None of my "Check this folder for new messages" options are checked.

You can update all folders at once by clicking File, Offline, Download/Sync Now... or File, Offline, Work Offline. The former option asks if you want to go offline following the sync. When you come back from Offline, the sync happens again.

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