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I can not thank developer enough for making such a useful addon. Only if there was a way to operate this addon through windows command line/cmd.exe, it would make life much much more simpler

Это отзыв для предыдущей версии этого дополнения (0.3.9). 

You are possibly looking for something like mbox-tools:
https://github.com/np/mbox-tools
which operates on Thunderbird's (highly dated) mail storage backend. I'm not sure if mbox-tools has dupe culling, though.