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Yes, you are right. jlink does not work with automatic modules. But using that plugin https://github.com/moditect/moditect you can easily transform almost any java library into a named module. It is a shame there are libraries under development, that have not been adapted to the java modular system.
For docker images, try to use google's "jib" project to build your docker images, because it makes the best use of the docker layered file system. You can use a "Dockerfile", but basically you will be moving your libraries around every time because they won't get pushed to a "lower" layer in the layered file system. https://github.com/GoogleContainerTools/jib
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