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This Addon is here for historical purpose and reference only.
The subfolder filter author has put comments up that discuss the "applyIncomingFilters" property.
As the author clear stated on their website (see home page URL above, or copy and paste http://www.stroppykitten.com/filterSubFolders/ )

EOL

EOL means End Of Life, no longer supported.

Please read the update.
(Don't use this filter on TBird 4 or above, it'll keep going back to Yes for any folder.)

Thanks Craig for the addon, it was a great one.

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Good extension, very useful , but can you provide a bit more details hot to make Thunderbird to apply filters to subfolder automatically.

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Hello,
great idea! Was just wondering if you could include a way to choose which filters should be run on all (or specified folders).
I have several filters and some I only need to run on the inbox (like moving certain emails) and others I like to run on all folders (like tagging of read,important etc..mails).
Would be awesome if you could include such a functionality!