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BOOK_EXTENSIONS controls what filetypes calibre recognizes as being ebooks. This list is not meant to be affected by file input plugins, which influence only what files calibre can convert.
As for creating the zip file, dont use github export, use calibre-customize. If you must use github export then simply move the files into the root of the repository.
And you need to have both __init__.py and the .txt file with the plugin import name in the root of the folder, for calibre to recognize the plugin, that is not going to change.
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