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Settings are now profile specfic. When you click the save button in the AnkiMorphs settings window, a file called ankimorphs_profile_settings.json will be saved to the anki profile folder. That file will then be read when Anki loads profiles.
The generators now ignores folder names when gathering input files. This means that you can have weird file structures like: fsrs.MD/fsrs.txt/fsrs.wiki.txt, and the file fsrs.wiki.txt will be gathered without AnkiMorphs crashing.