Most of my mail filters are applied directly on my server, where incoming mail is sorted in different IMAP folders, mostly depending on their target address (I use different addresses for every web service, yay catch all ).
I also have additional filters in Thunderbird since I was too lazy to install a mail filter with more features on my server. The problem with Thunderbird filters: per default they only run on the INBOX, which is kind of annoying with my given setup.
Once there was an add-on that did exactly this, but it is long dead.
But: turns out that Thunderbird has secretly had this feature all along. They simply never got around to adding a setting for it.
To activate filtering on all folders go to Preferences -> Tab Advanced -> Tab General -> Config Editor and promise to be careful.
There do a right click -> New -> String and name the new property
and as value enter
(both name and value are case sensitive)
(and don’t ask me why they didn’t choose a boolean property)
Tadaa! now all filters run on all folders in your account.