When a new message appears in the inbox, and you drag it to a subfolder (or any other account folder), ask the user to automatically create a filter for this message to this specific folder. Basically trigger the existing Creat Filter From Message option.
Example text: "Always move incoming messages from email@example.com to FolderX?"
answer options: "Yes/Not now/No, dont ask again"
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Like this addon I guess https://addons.thunderbird.net/en-US/thunderbird/addon/quickfilters/?src=cb-dl-mostpopular