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What's the alternative? Not installing the dependencies so the app doesn't work?

The alternative is vendoring the dependencies. That includes the JDK or Node runtime. With “modern” deployments you’ll see this with container based packaging that includes the runtimes either explicitly or via system packaged (in the container). The classic approach is copy the runtimes into your final application tarball.

Either way the runtime is baked into the app and gets deployed and tested with it as a core component. Runtime upgrades then become vanilla deployments.

Lots of options: containerization, downloading prebuilt binaries, downloading and building from source, or downloading, building, then packaging the artifacts and leaving somewhere centralized for deploy.

Using the language package manager - npm, cargo, etc.

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