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> Docker solves the problem of reliable deployment and dealing with dependencies.

Which, as noted, are problems that didn't used to exist and were created.

The thing that gets me is deploying JVM fat jars in Docker containers.

tar solves that problem too, it's a matter of what type of abstraction is a good fit for the problem at hand.

And shell scripts solve the problem of starting and stopping daemon, but not particularly well.

The boundary between a binary tarball and the rest of the system is very poorly defined.