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Git dependency is missings its own dependencies when npm prune is used

We’re using this library for our types: for the mysql2 library: https://github.com/types/mysql2

Since it isn’t officially on NPM as a package, it’s instead installed directly as a github: dependency. This usually works, but since upgrading our CI server to use npm@6.4.1 the dependency specified in its package.json for types/mysql is now being pruned when we run npm prune --production. This doesn’t seem to be reproducible locally; is there any case that would cause this deeper dependency to get deleted like this?

For now this is being fixed by just directly importing the types/mysql dependency, but that isn’t really ideal. Any word on how to diagnose or fix this issue would be appreciated!