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Now, you can use wine

Jar2Exe itself runs on Windows right now. You can use wine to start Jar2Exe command line mode, for example, in a script.sh :

wine /usr/local/bin/j2ewiz.exe \
    -o $TARGET \
    -m "$2" \
    -jar "(empty-jar)" \
    -encrypt \
    -keepflat "$FLATJAR" \
    $EMBED \
    -amd64 \
    -platform linux